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Commit af915b92 authored by Antony Carrard's avatar Antony Carrard
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Added default values

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UltrasoundBoneLabeler/Resources/UI/UltrasoundBoneLabeler.ui
+ 36
− 30
View file @ af915b92
......@@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>442</width>
<height>1159</height>
<height>1198</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
......@@ -562,41 +562,12 @@
</layout>
</widget>
</item>
<item>
<widget class="QPushButton" name="defaultParametersButton">
<property name="text">
<string>Default parameters</string>
</property>
</widget>
</item>
<item>
<widget class="ctkCollapsibleGroupBox" name="CollapsibleGroupBox_3">
<property name="title">
<string>Output parameters</string>
</property>
<layout class="QGridLayout" name="gridLayout_8">
<item row="0" column="1">
<widget class="ctkSliderWidget" name="SliderWidget">
<property name="decimals">
<number>0</number>
</property>
<property name="pageStep">
<double>1.000000000000000</double>
</property>
<property name="minimum">
<double>1.000000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="value">
<double>4.000000000000000</double>
</property>
<property name="SlicerParameterName" stdset="0">
<string>segmentationThickness</string>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="label_15">
<property name="text">
......@@ -640,6 +611,35 @@
</layout>
</widget>
</item>
<item row="0" column="1">
<widget class="ctkSliderWidget" name="SliderWidget">
<property name="decimals">
<number>0</number>
</property>
<property name="pageStep">
<double>1.000000000000000</double>
</property>
<property name="minimum">
<double>1.000000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="value">
<double>4.000000000000000</double>
</property>
<property name="SlicerParameterName" stdset="0">
<string>segmentationThickness</string>
</property>
</widget>
</item>
<item row="2" column="0" colspan="2">
<widget class="QPushButton" name="defaultParametersButton">
<property name="text">
<string>Default parameters</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
......@@ -789,6 +789,9 @@
<string>vtkMRMLSegmentationNode</string>
</stringlist>
</property>
<property name="showChildNodeTypes">
<bool>false</bool>
</property>
<property name="hideChildNodeTypes">
<stringlist notr="true"/>
</property>
......@@ -813,6 +816,9 @@
<string>vtkMRMLScalarVolumeNode</string>
</stringlist>
</property>
<property name="showChildNodeTypes">
<bool>false</bool>
</property>
<property name="hideChildNodeTypes">
<stringlist notr="true"/>
</property>
......
UltrasoundBoneLabeler/UltrasoundBoneLabeler.py
+ 65
− 25
View file @ af915b92
......@@ -20,6 +20,19 @@ from slicer import vtkMRMLScalarVolumeNode, vtkMRMLSegmentationNode, vtkMRMLVect
from Logic import bone_probability_mapping, bone_surface_identification, files_manager
# Default parameters constants
GAUSSIAN_KERNEL_SIZE = 25
BINARY_THRESHOLD = 0.2
TRANSDUCER_MARGIN = 0.1
SHADOW_SIGMA = 100
LOCAL_PHASE_SIGMA = 0.5
LOCAL_PHASE_WAVELENGTH = 2
BEST_LINE_THRESHOLD = 0.15
BEST_LINE_SIGMA = 10
LOG_KERNEL_SIZE = 31
SHADOW_NB_SIGMAS = 2
SEGMENTATION_THICKNESS = 4
MINIMUM_BONE_WIDTH = 0.4
#
# UltrasoundBoneLabeler
......@@ -116,24 +129,24 @@ class UltrasoundBoneLabelerParameterNode:
invertedVolume - The output volume that will contain the inverted thresholded volume.
"""
inputVector: vtkMRMLVectorVolumeNode
autoCropping: bool = False
resize: bool = False
autoCropping: bool = True
resize: bool = True
height: str = "256"
width: str = "256"
preprocessedVolume: vtkMRMLScalarVolumeNode
inputVolume: vtkMRMLScalarVolumeNode
gaussianKernelSize: Annotated[float, WithinRange(1, 63)] = 25
binaryThreshold: Annotated[float, WithinRange(0, 1)] = 0.2
transducerMargin: Annotated[float, WithinRange(0, 1)] = 0.1
shadowSigma: Annotated[float, WithinRange(1, 200)] = 100
localPhaseSigma: Annotated[float, WithinRange(0.1, 3)] = 0.5
localPhaseWavelength: Annotated[float, WithinRange(1, 6)] = 2
bestLineThreshold: Annotated[float, WithinRange(0, 1)] = 0.15
bestLineSigma: Annotated[float, WithinRange(1, 40)] = 10
LoGKernelSize: Annotated[float, WithinRange(1, 31)] = 31
shadowNbSigmas: Annotated[float, WithinRange(1, 4)] = 2
segmentationThickness: Annotated[float, WithinRange(1, 10)] = 4
minimumBoneWidth: Annotated[float, WithinRange(0, 1)] = 0.4
gaussianKernelSize: Annotated[float, WithinRange(1, 63)] = GAUSSIAN_KERNEL_SIZE
binaryThreshold: Annotated[float, WithinRange(0, 1)] = BINARY_THRESHOLD
transducerMargin: Annotated[float, WithinRange(0, 1)] = TRANSDUCER_MARGIN
shadowSigma: Annotated[float, WithinRange(1, 200)] = SHADOW_SIGMA
localPhaseSigma: Annotated[float, WithinRange(0.1, 3)] = LOCAL_PHASE_SIGMA
localPhaseWavelength: Annotated[float, WithinRange(1, 6)] = LOCAL_PHASE_WAVELENGTH
bestLineThreshold: Annotated[float, WithinRange(0, 1)] = BEST_LINE_THRESHOLD
bestLineSigma: Annotated[float, WithinRange(1, 40)] = BEST_LINE_SIGMA
LoGKernelSize: Annotated[float, WithinRange(1, 31)] = LOG_KERNEL_SIZE
shadowNbSigmas: Annotated[float, WithinRange(1, 4)] = SHADOW_NB_SIGMAS
segmentationThickness: Annotated[float, WithinRange(1, 10)] = SEGMENTATION_THICKNESS
minimumBoneWidth: Annotated[float, WithinRange(0, 1)] = MINIMUM_BONE_WIDTH
previewVolume: vtkMRMLScalarVolumeNode
outputSegmentation: vtkMRMLSegmentationNode
......@@ -189,6 +202,7 @@ class UltrasoundBoneLabelerWidget(ScriptedLoadableModuleWidget, VTKObservationMi
self.ui.preprocessButton.connect('clicked(bool)', self.onPreprocessButton)
self.ui.currentSliceButton.connect('clicked(bool)', self.onCurrentSliceButton)
self.ui.allVolumeButton.connect('clicked(bool)', self.onAllVolumeButton)
self.ui.defaultParametersButton.connect('clicked(bool)', self.onDefaultParametersButton)
self.ui.previewButton.connect('clicked(bool)', self.onPreviewButton)
# Make sure parameter node is initialized (needed for module reload)
......@@ -254,6 +268,22 @@ class UltrasoundBoneLabelerWidget(ScriptedLoadableModuleWidget, VTKObservationMi
if firstVectorNode:
self._parameterNode.inputVector = firstVectorNode
# Create a new volume for the preprocessed volume
if not self._parameterNode.preprocessedVolume:
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "Preprocessed Volume")
self._parameterNode.preprocessedVolume = volumeNode
# Create a new volume for the preview
if not self._parameterNode.previewVolume:
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "Preview Volume")
self._parameterNode.previewVolume = volumeNode
# If no segmentation exists, create a new one
if not self._parameterNode.outputSegmentation:
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode", "Segmentation")
self._parameterNode.outputSegmentation = segmentationNode
if self._parameterNode.inputVolume:
self.onAllVolumeButton()
......@@ -355,15 +385,6 @@ class UltrasoundBoneLabelerWidget(ScriptedLoadableModuleWidget, VTKObservationMi
# Refresh the input volume selector
self._parameterNode.inputVolume = self._parameterNode.preprocessedVolume
def onDefaultParametersButton(self) -> None:
"""
Run processing when user clicks "DefaultParameters" button.
"""
with slicer.util.tryWithErrorDisplay("Failed to compute results.", waitCursor=True):
pass # TODO put the default parameters values
def onCurrentSliceButton(self) -> None:
"""
Run processing when user clicks "Preprocess" button.
......@@ -388,6 +409,25 @@ class UltrasoundBoneLabelerWidget(ScriptedLoadableModuleWidget, VTKObservationMi
self.ui.rangeSlices.minimumValue = self.ui.rangeSlices.minimum
self.ui.rangeSlices.maximumValue = self.ui.rangeSlices.maximum
def onDefaultParametersButton(self) -> None:
"""
Run processing when user clicks "DefaultParameters" button.
"""
with slicer.util.tryWithErrorDisplay("Failed to compute results.", waitCursor=True):
self._parameterNode.gaussianKernelSize = GAUSSIAN_KERNEL_SIZE
self._parameterNode.binaryThreshold = BINARY_THRESHOLD
self._parameterNode.transducerMargin = TRANSDUCER_MARGIN
self._parameterNode.shadowSigma = SHADOW_SIGMA
self._parameterNode.localPhaseSigma = LOCAL_PHASE_SIGMA
self._parameterNode.localPhaseWavelength = LOCAL_PHASE_WAVELENGTH
self._parameterNode.bestLineThreshold = BEST_LINE_THRESHOLD
self._parameterNode.bestLineSigma = BEST_LINE_SIGMA
self._parameterNode.LoGKernelSize = LOG_KERNEL_SIZE
self._parameterNode.shadowNbSigmas = SHADOW_NB_SIGMAS
self._parameterNode.segmentationThickness = SEGMENTATION_THICKNESS
self._parameterNode.minimumBoneWidth = MINIMUM_BONE_WIDTH
self.onAllVolumeButton()
def onPreviewButton(self) -> None:
"""
......@@ -529,7 +569,7 @@ class UltrasoundBoneLabelerLogic(ScriptedLoadableModuleLogic):
localPhaseSigma,
localPhaseWavelength)
boneSurfId = bone_surface_identification.BoneSurfaceIdentification((9, 15),
boneSurfId = bone_surface_identification.BoneSurfaceIdentification((1, 1),
bestLineThreshold,
bestLineSigma,
minimumBoneWidth,
......@@ -537,7 +577,7 @@ class UltrasoundBoneLabelerLogic(ScriptedLoadableModuleLogic):
# If a segmentation already exists, start from it
segment = outputSegmentation.GetSegmentation().GetSegment(segmentName)
if segment:
if segment and 'self.tracedLabel3D' in locals():
self.tracedLabel3D = slicer.util.arrayFromSegmentBinaryLabelmap(outputSegmentation, segmentName, inputVolume).astype(np.uint8)[:, ::-1, ::-1]
# Otherwise instanciate the arrays
......
UltrasoundBoneLabeler/__pycache__/UltrasoundBoneLabeler.cpython-39.pyc
+ 0
− 0
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