diff --git a/Modules/Segmentation/Interactions/mitkContourTool.cpp b/Modules/Segmentation/Interactions/mitkContourTool.cpp
index 7c16912f7b..109fd68bdc 100644
--- a/Modules/Segmentation/Interactions/mitkContourTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkContourTool.cpp
@@ -1,197 +1,190 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkContourTool.h"
#include "mitkAbstractTransformGeometry.h"
#include "mitkOverwriteDirectedPlaneImageFilter.h"
#include "mitkOverwriteSliceImageFilter.h"
#include "mitkToolManager.h"
#include "mitkBaseRenderer.h"
#include "mitkRenderingManager.h"
//#include "mitkProperties.h"
//#include "mitkPlanarCircle.h"
#include "mitkLabelSetImage.h"
#include "mitkInteractionEvent.h"
#include "mitkStateMachineAction.h"
mitk::ContourTool::ContourTool(int paintingPixelValue)
: FeedbackContourTool("PressMoveReleaseWithCTRLInversion"),
- m_PaintingPixelValue(paintingPixelValue),
- m_CurrentLabelID(1)
+ m_PaintingPixelValue(paintingPixelValue)
{
}
mitk::ContourTool::~ContourTool()
{
}
void mitk::ContourTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
CONNECT_FUNCTION("InvertLogic", OnInvertLogic);
}
void mitk::ContourTool::Activated()
{
Superclass::Activated();
}
void mitk::ContourTool::Deactivated()
{
Superclass::Deactivated();
}
/**
Just show the contour, insert the first point.
*/
void mitk::ContourTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel *contour = FeedbackContourTool::GetFeedbackContour();
// Clear feedback contour
contour->Initialize();
// expand time bounds because our contour was initialized
contour->Expand(timestep + 1);
// draw as a closed contour
contour->SetClosed(true, timestep);
// add first mouse position
mitk::Point3D point = positionEvent->GetPositionInWorld();
contour->AddVertex(point, timestep);
FeedbackContourTool::SetFeedbackContourVisible(true);
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
/**
Insert the point to the feedback contour.
*/
void mitk::ContourTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel *contour = FeedbackContourTool::GetFeedbackContour();
mitk::Point3D point = positionEvent->GetPositionInWorld();
contour->AddVertex(point, timestep);
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
/**
Close the contour, project it to the image slice and fill it in 2D.
*/
void mitk::ContourTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
// const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || !planeGeometry)
return;
- // Check if it is a multilabel-image
- // If yes, get the new drawing color from it.
- // Otherwise nothing happens.
+ // Check if it is a multilabel-image. If yes, get the new drawing color from it.
auto *labelSetImage = dynamic_cast<LabelSetImage *>(image);
- if (labelSetImage)
+ int activePixelValue = 1;
+ if (nullptr != labelSetImage)
{
- mitk::Label *label = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer());
- m_CurrentLabelID = label->GetValue();
- }
- else
- {
- m_CurrentLabelID = 1;
+ activePixelValue = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer())->GetValue();
}
const auto *abstractTransformGeometry(
dynamic_cast<const AbstractTransformGeometry *>(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || abstractTransformGeometry)
return;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage(positionEvent, image);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour = FeedbackContourTool::GetFeedbackContour();
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, true, false); // true: actually no idea why this is neccessary, but it works :-(
if (projectedContour.IsNull())
return;
int timestep = positionEvent->GetSender()->GetTimeStep();
// m_PaintingPixelValue only decides whether to paint or erase
mitk::ContourModelUtils::FillContourInSlice(
- projectedContour, timestep, slice, image, (m_PaintingPixelValue * m_CurrentLabelID));
+ projectedContour, timestep, slice, image, (m_PaintingPixelValue * activePixelValue));
// this->WriteBackSegmentationResult(positionEvent, slice);
SegTool2D::WriteBackSegmentationResult(positionEvent, slice);
// 4. Make sure the result is drawn again --> is visible then.
assert(positionEvent->GetSender()->GetRenderWindow());
}
/**
Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0.
*/
void mitk::ContourTool::OnInvertLogic(StateMachineAction *, InteractionEvent *)
{
// Inversion only for 0 and 1 as painting values
if (m_PaintingPixelValue == 1)
{
m_PaintingPixelValue = 0;
FeedbackContourTool::SetFeedbackContourColor(1.0, 0.0, 0.0);
}
else if (m_PaintingPixelValue == 0)
{
m_PaintingPixelValue = 1;
FeedbackContourTool::SetFeedbackContourColorDefault();
}
}
diff --git a/Modules/Segmentation/Interactions/mitkContourTool.h b/Modules/Segmentation/Interactions/mitkContourTool.h
index 88b0317a83..23e7d7a79c 100644
--- a/Modules/Segmentation/Interactions/mitkContourTool.h
+++ b/Modules/Segmentation/Interactions/mitkContourTool.h
@@ -1,72 +1,71 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkContourTool_h_Included
#define mitkContourTool_h_Included
#include "mitkCommon.h"
#include "mitkFeedbackContourTool.h"
#include <MitkSegmentationExports.h>
namespace mitk
{
class Image;
class StateMachineAction;
class InteractionEvent;
/**
\brief Simple contour filling tool.
\sa FeedbackContourTool
\sa ExtractImageFilter
\sa OverwriteSliceImageFilter
\ingroup Interaction
\ingroup ToolManagerEtAl
Fills a visible contour (from FeedbackContourTool) during mouse dragging. When the mouse button
is released, ContourTool tries to extract a slice from the working image and fill in
the (filled) contour as a binary image.
The painting "color" is defined by m_PaintingPixelValue, which is set in the constructor
(by sub-classes) or during some event (e.g. in OnInvertLogic - when CTRL is pressed).
\warning Only to be instantiated by mitk::ToolManager.
$Author$
*/
class MITKSEGMENTATION_EXPORT ContourTool : public FeedbackContourTool
{
public:
mitkClassMacro(ContourTool, FeedbackContourTool);
protected:
ContourTool(int paintingPixelValue = 1); // purposely hidden
~ContourTool() override;
void Activated() override;
void Deactivated() override;
virtual void OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent);
virtual void OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent);
virtual void OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent);
virtual void OnInvertLogic(StateMachineAction *, InteractionEvent *interactionEvent);
void ConnectActionsAndFunctions() override;
int m_PaintingPixelValue;
- int m_CurrentLabelID;
};
} // namespace
#endif
diff --git a/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp
index 1cb67b63d1..f3bb9b4500 100644
--- a/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp
@@ -1,594 +1,594 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPaintbrushTool.h"
#include "ipSegmentation.h"
#include "mitkAbstractTransformGeometry.h"
#include "mitkBaseRenderer.h"
#include "mitkImageDataItem.h"
#include "mitkOverwriteSliceImageFilter.h"
#include "mitkToolManager.h"
#include "mitkContourModelUtils.h"
#include "mitkLabelSetImage.h"
#include "mitkLevelWindowProperty.h"
int mitk::PaintbrushTool::m_Size = 1;
mitk::PaintbrushTool::PaintbrushTool(int paintingPixelValue)
: FeedbackContourTool("PressMoveReleaseWithCTRLInversionAllMouseMoves"),
m_PaintingPixelValue(paintingPixelValue),
m_LastContourSize(0) // other than initial mitk::PaintbrushTool::m_Size (around l. 28)
{
m_MasterContour = ContourModel::New();
m_MasterContour->Initialize();
m_CurrentPlane = nullptr;
m_WorkingNode = DataNode::New();
m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1)));
m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true));
}
mitk::PaintbrushTool::~PaintbrushTool()
{
}
void mitk::PaintbrushTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnPrimaryButtonPressedMoved);
CONNECT_FUNCTION("MouseMove", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
CONNECT_FUNCTION("InvertLogic", OnInvertLogic);
}
void mitk::PaintbrushTool::Activated()
{
Superclass::Activated();
FeedbackContourTool::SetFeedbackContourVisible(true);
SizeChanged.Send(m_Size);
m_ToolManager->WorkingDataChanged +=
mitk::MessageDelegate<mitk::PaintbrushTool>(this, &mitk::PaintbrushTool::OnToolManagerWorkingDataModified);
}
void mitk::PaintbrushTool::Deactivated()
{
FeedbackContourTool::SetFeedbackContourVisible(false);
if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_WorkingSlice = nullptr;
m_CurrentPlane = nullptr;
m_ToolManager->WorkingDataChanged -=
mitk::MessageDelegate<mitk::PaintbrushTool>(this, &mitk::PaintbrushTool::OnToolManagerWorkingDataModified);
Superclass::Deactivated();
}
void mitk::PaintbrushTool::SetSize(int value)
{
m_Size = value;
}
mitk::Point2D mitk::PaintbrushTool::upperLeft(mitk::Point2D p)
{
p[0] -= 0.5;
p[1] += 0.5;
return p;
}
void mitk::PaintbrushTool::UpdateContour(const InteractionPositionEvent *positionEvent)
{
// MITK_INFO<<"Update...";
// examine stateEvent and create a contour that matches the pixel mask that we are going to draw
// mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
// const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent)
return;
// Get Spacing of current Slice
// mitk::Vector3D vSpacing = m_WorkingSlice->GetSlicedGeometry()->GetPlaneGeometry(0)->GetSpacing();
//
// Draw a contour in Square according to selected brush size
//
int radius = (m_Size) / 2;
float fradius = static_cast<float>(m_Size) / 2.0f;
ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
// estimate center point of the brush ( relative to the pixel the mouse points on )
// -- left upper corner for even sizes,
// -- midpoint for uneven sizes
mitk::Point2D centerCorrection;
centerCorrection.Fill(0);
// even --> correction of [+0.5, +0.5]
bool evenSize = ((m_Size % 2) == 0);
if (evenSize)
{
centerCorrection[0] += 0.5;
centerCorrection[1] += 0.5;
}
// we will compute the control points for the upper left quarter part of a circle contour
std::vector<mitk::Point2D> quarterCycleUpperRight;
std::vector<mitk::Point2D> quarterCycleLowerRight;
std::vector<mitk::Point2D> quarterCycleLowerLeft;
std::vector<mitk::Point2D> quarterCycleUpperLeft;
mitk::Point2D curPoint;
bool curPointIsInside = true;
curPoint[0] = 0;
curPoint[1] = radius;
quarterCycleUpperRight.push_back(upperLeft(curPoint));
// to estimate if a pixel is inside the circle, we need to compare against the 'outer radius'
// i.e. the distance from the midpoint [0,0] to the border of the pixel [0,radius]
// const float outer_radius = static_cast<float>(radius) + 0.5;
while (curPoint[1] > 0)
{
// Move right until pixel is outside circle
float curPointX_squared = 0.0f;
float curPointY_squared = (curPoint[1] - centerCorrection[1]) * (curPoint[1] - centerCorrection[1]);
while (curPointIsInside)
{
// increment posX and chec
curPoint[0]++;
curPointX_squared = (curPoint[0] - centerCorrection[0]) * (curPoint[0] - centerCorrection[0]);
const float len = sqrt(curPointX_squared + curPointY_squared);
if (len > fradius)
{
// found first Pixel in this horizontal line, that is outside the circle
curPointIsInside = false;
}
}
quarterCycleUpperRight.push_back(upperLeft(curPoint));
// Move down until pixel is inside circle
while (!curPointIsInside)
{
// increment posX and chec
curPoint[1]--;
curPointY_squared = (curPoint[1] - centerCorrection[1]) * (curPoint[1] - centerCorrection[1]);
const float len = sqrt(curPointX_squared + curPointY_squared);
if (len <= fradius)
{
// found first Pixel in this horizontal line, that is outside the circle
curPointIsInside = true;
quarterCycleUpperRight.push_back(upperLeft(curPoint));
}
// Quarter cycle is full, when curPoint y position is 0
if (curPoint[1] <= 0)
break;
}
}
// QuarterCycle is full! Now copy quarter cycle to other quarters.
if (!evenSize)
{
std::vector<mitk::Point2D>::const_iterator it = quarterCycleUpperRight.begin();
while (it != quarterCycleUpperRight.end())
{
mitk::Point2D p;
p = *it;
// the contour points in the lower right corner have same position but with negative y values
p[1] *= -1;
quarterCycleLowerRight.push_back(p);
// the contour points in the lower left corner have same position
// but with both x,y negative
p[0] *= -1;
quarterCycleLowerLeft.push_back(p);
// the contour points in the upper left corner have same position
// but with x negative
p[1] *= -1;
quarterCycleUpperLeft.push_back(p);
it++;
}
}
else
{
std::vector<mitk::Point2D>::const_iterator it = quarterCycleUpperRight.begin();
while (it != quarterCycleUpperRight.end())
{
mitk::Point2D p, q;
p = *it;
q = p;
// the contour points in the lower right corner have same position but with negative y values
q[1] *= -1;
// correct for moved offset if size even = the midpoint is not the midpoint of the current pixel
// but its upper rigt corner
q[1] += 1;
quarterCycleLowerRight.push_back(q);
q = p;
// the contour points in the lower left corner have same position
// but with both x,y negative
q[1] = -1.0f * q[1] + 1;
q[0] = -1.0f * q[0] + 1;
quarterCycleLowerLeft.push_back(q);
// the contour points in the upper left corner have same position
// but with x negative
q = p;
q[0] *= -1;
q[0] += 1;
quarterCycleUpperLeft.push_back(q);
it++;
}
}
// fill contour with poins in right ordering, starting with the upperRight block
mitk::Point3D tempPoint;
for (unsigned int i = 0; i < quarterCycleUpperRight.size(); i++)
{
tempPoint[0] = quarterCycleUpperRight[i][0];
tempPoint[1] = quarterCycleUpperRight[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
// the lower right has to be parsed in reverse order
for (int i = quarterCycleLowerRight.size() - 1; i >= 0; i--)
{
tempPoint[0] = quarterCycleLowerRight[i][0];
tempPoint[1] = quarterCycleLowerRight[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
for (unsigned int i = 0; i < quarterCycleLowerLeft.size(); i++)
{
tempPoint[0] = quarterCycleLowerLeft[i][0];
tempPoint[1] = quarterCycleLowerLeft[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
// the upper left also has to be parsed in reverse order
for (int i = quarterCycleUpperLeft.size() - 1; i >= 0; i--)
{
tempPoint[0] = quarterCycleUpperLeft[i][0];
tempPoint[1] = quarterCycleUpperLeft[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
m_MasterContour = contourInImageIndexCoordinates;
}
/**
Just show the contour, get one point as the central point and add surrounding points to the contour.
*/
void mitk::PaintbrushTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
if (m_WorkingSlice.IsNull())
return;
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_WorkingSlice->GetGeometry()->WorldToIndex(positionEvent->GetPositionInWorld(), m_LastPosition);
// create new working node
// a fresh node is needed to only display the actual drawing process for
// the undo function
if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_WorkingSlice = nullptr;
m_CurrentPlane = nullptr;
m_WorkingNode = DataNode::New();
m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1)));
m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true));
this->m_WorkingNode->SetVisibility(true);
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
m_MasterContour->SetClosed(true);
this->MouseMoved(interactionEvent, true);
}
void mitk::PaintbrushTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
MouseMoved(interactionEvent, false);
}
void mitk::PaintbrushTool::OnPrimaryButtonPressedMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
MouseMoved(interactionEvent, true);
}
/**
Insert the point to the feedback contour,finish to build the contour and at the same time the painting function
*/
void mitk::PaintbrushTool::MouseMoved(mitk::InteractionEvent *interactionEvent, bool leftMouseButtonPressed)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
CheckIfCurrentSliceHasChanged(positionEvent);
if (m_LastContourSize != m_Size)
{
UpdateContour(positionEvent);
m_LastContourSize = m_Size;
}
Point3D worldCoordinates = positionEvent->GetPositionInWorld();
Point3D indexCoordinates;
m_WorkingSlice->GetGeometry()->WorldToIndex(worldCoordinates, indexCoordinates);
// round to nearest voxel center (abort if this hasn't changed)
if (m_Size % 2 == 0) // even
{
indexCoordinates[0] = std::round(indexCoordinates[0]);
indexCoordinates[1] = std::round(indexCoordinates[1]);
}
else // odd
{
indexCoordinates[0] = std::round(indexCoordinates[0]);
indexCoordinates[1] = std::round(indexCoordinates[1]);
}
static Point3D lastPos; // uninitialized: if somebody finds out how this can be initialized in a one-liner, tell me
if (fabs(indexCoordinates[0] - lastPos[0]) > mitk::eps || fabs(indexCoordinates[1] - lastPos[1]) > mitk::eps ||
fabs(indexCoordinates[2] - lastPos[2]) > mitk::eps || leftMouseButtonPressed)
{
lastPos = indexCoordinates;
}
else
{
return;
}
int t = positionEvent->GetSender()->GetTimeStep();
auto contour = ContourModel::New();
contour->SetClosed(true);
auto it = m_MasterContour->Begin();
auto end = m_MasterContour->End();
while (it != end)
{
auto point = (*it)->Coordinates;
point[0] += indexCoordinates[0];
point[1] += indexCoordinates[1];
contour->AddVertex(point);
++it;
}
if (leftMouseButtonPressed)
{
const double dist = indexCoordinates.EuclideanDistanceTo(m_LastPosition);
const double radius = static_cast<double>(m_Size) / 2.0;
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
Image::Pointer image = dynamic_cast<Image *>(workingNode->GetData());
- auto *labelImage = dynamic_cast<LabelSetImage *>(image.GetPointer());
+ auto *labelSetImage = dynamic_cast<LabelSetImage *>(image.GetPointer());
- int activeColor = 1;
- if (labelImage)
+ int activePixelValue = 1;
+ if (nullptr != labelSetImage)
{
- activeColor = labelImage->GetActiveLabel(labelImage->GetActiveLayer())->GetValue();
+ activePixelValue = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer())->GetValue();
}
// m_PaintingPixelValue only decides whether to paint or erase
mitk::ContourModelUtils::FillContourInSlice(
- contour, m_WorkingSlice, image, m_PaintingPixelValue * activeColor);
+ contour, m_WorkingSlice, image, m_PaintingPixelValue * activePixelValue);
m_WorkingNode->SetData(m_WorkingSlice);
m_WorkingNode->Modified();
// if points are >= radius away draw rectangle to fill empty holes
// in between the 2 points
if (dist > radius)
{
const mitk::Point3D ¤tPos = indexCoordinates;
mitk::Point3D direction;
mitk::Point3D vertex;
mitk::Point3D normal;
direction[0] = indexCoordinates[0] - m_LastPosition[0];
direction[1] = indexCoordinates[1] - m_LastPosition[1];
direction[2] = indexCoordinates[2] - m_LastPosition[2];
direction[0] = direction.GetVnlVector().normalize()[0];
direction[1] = direction.GetVnlVector().normalize()[1];
direction[2] = direction.GetVnlVector().normalize()[2];
// 90 degrees rotation of direction
normal[0] = -1.0 * direction[1];
normal[1] = direction[0];
contour->Clear();
// upper left corner
vertex[0] = m_LastPosition[0] + (normal[0] * radius);
vertex[1] = m_LastPosition[1] + (normal[1] * radius);
contour->AddVertex(vertex);
// upper right corner
vertex[0] = currentPos[0] + (normal[0] * radius);
vertex[1] = currentPos[1] + (normal[1] * radius);
contour->AddVertex(vertex);
// lower right corner
vertex[0] = currentPos[0] - (normal[0] * radius);
vertex[1] = currentPos[1] - (normal[1] * radius);
contour->AddVertex(vertex);
// lower left corner
vertex[0] = m_LastPosition[0] - (normal[0] * radius);
vertex[1] = m_LastPosition[1] - (normal[1] * radius);
contour->AddVertex(vertex);
- mitk::ContourModelUtils::FillContourInSlice(contour, m_WorkingSlice, image, m_PaintingPixelValue * activeColor);
+ mitk::ContourModelUtils::FillContourInSlice(contour, m_WorkingSlice, image, m_PaintingPixelValue * activePixelValue);
m_WorkingNode->SetData(m_WorkingSlice);
m_WorkingNode->Modified();
}
}
else
{
// switched from different renderwindow
// no activate hover highlighting. Otherwise undo / redo wont work
this->m_WorkingNode->SetVisibility(false);
}
m_LastPosition = indexCoordinates;
// visualize contour
ContourModel::Pointer displayContour = FeedbackContourTool::GetFeedbackContour();
displayContour->Clear();
ContourModel::Pointer tmp =
FeedbackContourTool::BackProjectContourFrom2DSlice(m_WorkingSlice->GetGeometry(), contour);
// copy transformed contour into display contour
it = tmp->Begin();
end = tmp->End();
while (it != end)
{
Point3D point = (*it)->Coordinates;
displayContour->AddVertex(point, t);
it++;
}
m_FeedbackContourNode->GetData()->Modified();
assert(positionEvent->GetSender()->GetRenderWindow());
RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::PaintbrushTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// When mouse is released write segmentationresult back into image
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice->Clone());
// deactivate visibility of helper node
m_WorkingNode->SetVisibility(false);
RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
/**
Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0.
*/
void mitk::PaintbrushTool::OnInvertLogic(StateMachineAction *, InteractionEvent *)
{
// Inversion only for 0 and 1 as painting values
if (m_PaintingPixelValue == 1)
{
m_PaintingPixelValue = 0;
FeedbackContourTool::SetFeedbackContourColor(1.0, 0.0, 0.0);
}
else if (m_PaintingPixelValue == 0)
{
m_PaintingPixelValue = 1;
FeedbackContourTool::SetFeedbackContourColorDefault();
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(const InteractionPositionEvent *event)
{
const PlaneGeometry *planeGeometry((event->GetSender()->GetCurrentWorldPlaneGeometry()));
const auto *abstractTransformGeometry(
dynamic_cast<const AbstractTransformGeometry *>(event->GetSender()->GetCurrentWorldPlaneGeometry()));
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
Image::Pointer image = dynamic_cast<Image *>(workingNode->GetData());
if (!image || !planeGeometry || abstractTransformGeometry)
return;
if (m_CurrentPlane.IsNull() || m_WorkingSlice.IsNull())
{
m_CurrentPlane = planeGeometry;
m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone();
m_WorkingNode->ReplaceProperty("color", workingNode->GetProperty("color"));
m_WorkingNode->SetData(m_WorkingSlice);
}
else
{
bool isSameSlice(false);
isSameSlice = mitk::MatrixEqualElementWise(planeGeometry->GetIndexToWorldTransform()->GetMatrix(),
m_CurrentPlane->GetIndexToWorldTransform()->GetMatrix());
isSameSlice = mitk::Equal(planeGeometry->GetIndexToWorldTransform()->GetOffset(),
m_CurrentPlane->GetIndexToWorldTransform()->GetOffset());
if (!isSameSlice)
{
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_CurrentPlane = nullptr;
m_WorkingSlice = nullptr;
m_WorkingNode = nullptr;
m_CurrentPlane = planeGeometry;
m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone();
m_WorkingNode = mitk::DataNode::New();
m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1)));
m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true));
m_WorkingNode->SetData(m_WorkingSlice);
// So that the paintbrush contour vanished in the previous render window
RenderingManager::GetInstance()->RequestUpdateAll();
}
}
if (!m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
{
m_WorkingNode->SetProperty("outline binary", mitk::BoolProperty::New(true));
m_WorkingNode->SetProperty("color", workingNode->GetProperty("color"));
m_WorkingNode->SetProperty("name", mitk::StringProperty::New("Paintbrush_Node"));
m_WorkingNode->SetProperty("helper object", mitk::BoolProperty::New(true));
m_WorkingNode->SetProperty("opacity", mitk::FloatProperty::New(0.8));
m_WorkingNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
m_WorkingNode->SetVisibility(
false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3")));
m_ToolManager->GetDataStorage()->Add(m_WorkingNode);
}
}
void mitk::PaintbrushTool::OnToolManagerWorkingDataModified()
{
// Here we simply set the current working slice to null. The next time the mouse is moved
// within a renderwindow a new slice will be extracted from the new working data
m_WorkingSlice = nullptr;
}
diff --git a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp
index 988d50cc5c..5bcc0fa99a 100644
--- a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp
@@ -1,664 +1,664 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkRegionGrowingTool.h"
#include "mitkApplicationCursor.h"
#include "mitkBaseRenderer.h"
#include "mitkImageDataItem.h"
#include "mitkImageToContourModelFilter.h"
#include "mitkOverwriteSliceImageFilter.h"
#include "mitkRegionGrowingTool.xpm"
#include "mitkRenderingManager.h"
#include "mitkToolManager.h"
#include "mitkExtractDirectedPlaneImageFilterNew.h"
#include "mitkLabelSetImage.h"
#include "mitkOverwriteDirectedPlaneImageFilter.h"
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
// ITK
#include "mitkITKImageImport.h"
#include "mitkImageAccessByItk.h"
#include <itkConnectedComponentImageFilter.h>
#include <itkConnectedThresholdImageFilter.h>
#include <itkImageRegionIteratorWithIndex.h>
#include <itkNeighborhoodIterator.h>
#include <itkImageDuplicator.h>
#include <limits>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, RegionGrowingTool, "Region growing tool");
}
#define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a)))
mitk::RegionGrowingTool::RegionGrowingTool()
: FeedbackContourTool("PressMoveRelease"),
m_SeedValue(0),
m_ScreenYDifference(0),
m_ScreenXDifference(0),
m_MouseDistanceScaleFactor(0.5),
m_PaintingPixelValue(0),
m_FillFeedbackContour(true),
m_ConnectedComponentValue(1)
{
}
mitk::RegionGrowingTool::~RegionGrowingTool()
{
}
void mitk::RegionGrowingTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
}
const char **mitk::RegionGrowingTool::GetXPM() const
{
return mitkRegionGrowingTool_xpm;
}
us::ModuleResource mitk::RegionGrowingTool::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("RegionGrowing_48x48.png");
return resource;
}
us::ModuleResource mitk::RegionGrowingTool::GetCursorIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("RegionGrowing_Cursor_32x32.png");
return resource;
}
const char *mitk::RegionGrowingTool::GetName() const
{
return "Region Growing";
}
void mitk::RegionGrowingTool::Activated()
{
Superclass::Activated();
}
void mitk::RegionGrowingTool::Deactivated()
{
Superclass::Deactivated();
}
// Get the average pixel value of square/cube with radius=neighborhood around index
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::GetNeighborhoodAverage(const itk::Image<TPixel, imageDimension> *itkImage,
const itk::Index<imageDimension>& index,
ScalarType *result,
unsigned int neighborhood)
{
// maybe assert that image dimension is only 2 or 3?
auto neighborhoodInt = (int)neighborhood;
TPixel averageValue(0);
unsigned int numberOfPixels = (2 * neighborhood + 1) * (2 * neighborhood + 1);
if (imageDimension == 3)
{
numberOfPixels *= (2 * neighborhood + 1);
}
MITK_DEBUG << "Getting neighborhood of " << numberOfPixels << " pixels around " << index;
itk::Index<imageDimension> currentIndex;
for (int i = (0 - neighborhoodInt); i <= neighborhoodInt; ++i)
{
currentIndex[0] = index[0] + i;
for (int j = (0 - neighborhoodInt); j <= neighborhoodInt; ++j)
{
currentIndex[1] = index[1] + j;
if (imageDimension == 3)
{
for (int k = (0 - neighborhoodInt); k <= neighborhoodInt; ++k)
{
currentIndex[2] = index[2] + k;
if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex))
{
averageValue += itkImage->GetPixel(currentIndex);
}
else
{
numberOfPixels -= 1;
}
}
}
else
{
if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex))
{
averageValue += itkImage->GetPixel(currentIndex);
}
else
{
numberOfPixels -= 1;
}
}
}
}
*result = (ScalarType)averageValue;
*result /= numberOfPixels;
}
// Check whether index lies inside a segmentation
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::IsInsideSegmentation(const itk::Image<TPixel, imageDimension> *itkImage,
const itk::Index<imageDimension>& index,
bool *result)
{
if (itkImage->GetPixel(index) > 0)
{
*result = true;
}
else
{
*result = false;
}
}
// Do the region growing (i.e. call an ITK filter that does it)
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::StartRegionGrowing(const itk::Image<TPixel, imageDimension> *inputImage,
const itk::Index<imageDimension>& seedIndex,
const std::array<ScalarType, 2>& thresholds,
mitk::Image::Pointer &outputImage)
{
MITK_DEBUG << "Starting region growing at index " << seedIndex << " with lower threshold " << thresholds[0]
<< " and upper threshold " << thresholds[1];
typedef itk::Image<TPixel, imageDimension> InputImageType;
typedef itk::Image<DefaultSegmentationDataType, imageDimension> OutputImageType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> RegionGrowingFilterType;
typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// perform region growing in desired segmented region
regionGrower->SetInput(inputImage);
regionGrower->SetSeed(seedIndex);
regionGrower->SetLower(thresholds[0]);
regionGrower->SetUpper(thresholds[1]);
try
{
regionGrower->Update();
}
catch (...)
{
return; // Should we do something?
}
typename OutputImageType::Pointer resultImage = regionGrower->GetOutput();
// Smooth result: Every pixel is replaced by the majority of the neighborhood
typedef itk::NeighborhoodIterator<OutputImageType> NeighborhoodIteratorType;
typedef itk::ImageRegionIterator<OutputImageType> ImageIteratorType;
typename NeighborhoodIteratorType::RadiusType radius;
radius.Fill(2); // for now, maybe make this something the user can adjust in the preferences?
typedef itk::ImageDuplicator< OutputImageType > DuplicatorType;
typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(resultImage);
duplicator->Update();
typename OutputImageType::Pointer resultDup = duplicator->GetOutput();
NeighborhoodIteratorType neighborhoodIterator(radius, resultDup, resultDup->GetRequestedRegion());
ImageIteratorType imageIterator(resultImage, resultImage->GetRequestedRegion());
for (neighborhoodIterator.GoToBegin(), imageIterator.GoToBegin(); !neighborhoodIterator.IsAtEnd();
++neighborhoodIterator, ++imageIterator)
{
DefaultSegmentationDataType voteYes(0);
DefaultSegmentationDataType voteNo(0);
for (unsigned int i = 0; i < neighborhoodIterator.Size(); ++i)
{
if (neighborhoodIterator.GetPixel(i) > 0)
{
voteYes += 1;
}
else
{
voteNo += 1;
}
}
if (voteYes > voteNo)
{
imageIterator.Set(1);
}
else
{
imageIterator.Set(0);
}
}
if (resultImage.IsNull())
{
MITK_DEBUG << "Region growing result is empty.";
}
// Can potentially have multiple regions, use connected component image filter to label disjunct regions
typedef itk::ConnectedComponentImageFilter<OutputImageType, OutputImageType> ConnectedComponentImageFilterType;
typename ConnectedComponentImageFilterType::Pointer connectedComponentFilter =
ConnectedComponentImageFilterType::New();
connectedComponentFilter->SetInput(resultImage);
connectedComponentFilter->Update();
typename OutputImageType::Pointer resultImageCC = connectedComponentFilter->GetOutput();
m_ConnectedComponentValue = resultImageCC->GetPixel(seedIndex);
outputImage = mitk::GrabItkImageMemory(resultImageCC);
}
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::CalculateInitialThresholds(const itk::Image<TPixel, imageDimension>*)
{
LevelWindow levelWindow;
m_ToolManager->GetReferenceData(0)->GetLevelWindow(levelWindow);
m_ThresholdExtrema[0] = static_cast<ScalarType>(std::numeric_limits<TPixel>::lowest());
m_ThresholdExtrema[1] = static_cast<ScalarType>(std::numeric_limits<TPixel>::max());
const ScalarType lowerWindowBound = std::max(m_ThresholdExtrema[0], levelWindow.GetLowerWindowBound());
const ScalarType upperWindowBound = std::min(m_ThresholdExtrema[1], levelWindow.GetUpperWindowBound());
if (m_SeedValue < lowerWindowBound)
{
m_InitialThresholds = { m_ThresholdExtrema[0], lowerWindowBound };
}
else if (m_SeedValue > upperWindowBound)
{
m_InitialThresholds = { upperWindowBound, m_ThresholdExtrema[1] };
}
else
{
const ScalarType range = 0.1 * (upperWindowBound - lowerWindowBound); // 10% of the visible window
m_InitialThresholds[0] = std::min(std::max(lowerWindowBound, m_SeedValue - 0.5 * range), upperWindowBound - range);
m_InitialThresholds[1] = m_InitialThresholds[0] + range;
}
}
void mitk::RegionGrowingTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
MITK_DEBUG << "OnMousePressed";
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
m_LastScreenPosition = positionEvent->GetPointerPositionOnScreen();
// ReferenceSlice is from the underlying image, WorkingSlice from the active segmentation (can be empty)
m_ReferenceSlice = FeedbackContourTool::GetAffectedReferenceSlice(positionEvent);
m_WorkingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (m_WorkingSlice.IsNotNull()) // can't do anything without a working slice (i.e. a possibly empty segmentation)
{
MITK_DEBUG << "OnMousePressed: got working slice";
// 2. Determine if the user clicked inside or outside of the segmentation/working slice (i.e. the whole volume)
mitk::BaseGeometry::Pointer workingSliceGeometry;
workingSliceGeometry = m_WorkingSlice->GetGeometry();
workingSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), m_SeedPoint);
itk::Index<2> indexInWorkingSlice2D;
indexInWorkingSlice2D[0] = m_SeedPoint[0];
indexInWorkingSlice2D[1] = m_SeedPoint[1];
if (workingSliceGeometry->IsIndexInside(m_SeedPoint))
{
MITK_DEBUG << "OnMousePressed: point " << positionEvent->GetPositionInWorld() << " (index coordinates "
<< m_SeedPoint << ") is inside working slice";
// 3. determine the pixel value under the last click to determine what to do
bool inside(true);
AccessFixedDimensionByItk_2(m_WorkingSlice, IsInsideSegmentation, 2, indexInWorkingSlice2D, &inside);
m_PaintingPixelValue = inside ? 0 : 1;
if (inside)
{
MITK_DEBUG << "Clicked inside segmentation";
// For now, we're doing nothing when the user clicks inside the segmentation. Behaviour can be implemented via
// OnMousePressedInside()
// When you do, be sure to remove the m_PaintingPixelValue check in OnMouseMoved() and OnMouseReleased()
return;
}
else
{
MITK_DEBUG << "Clicked outside of segmentation";
OnMousePressedOutside(nullptr, interactionEvent);
}
}
}
}
// Use this to implement a behaviour for when the user clicks inside a segmentation (for example remove something)
// Old IpPic code is kept as comment for reference
void mitk::RegionGrowingTool::OnMousePressedInside()
{
// mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent
// );
// //const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent()); // checked in
// OnMousePressed
// // 3.1.1. Create a skeletonization of the segmentation and try to find a nice cut
// // apply the skeletonization-and-cut algorithm
// // generate contour to remove
// // set m_ReferenceSlice = nullptr so nothing will happen during mouse move
// // remember to fill the contour with 0 in mouserelease
// mitkIpPicDescriptor* segmentationHistory = ipMITKSegmentationCreateGrowerHistory( workingPicSlice,
// m_LastWorkingSeed, nullptr ); // free again
// if (segmentationHistory)
// {
// tCutResult cutContour = ipMITKSegmentationGetCutPoints( workingPicSlice, segmentationHistory,
// initialWorkingOffset ); // tCutResult is a ipSegmentation type
// mitkIpPicFree( segmentationHistory );
// if (cutContour.cutIt)
// {
// int timestep = positionEvent->GetSender()->GetTimeStep();
// // 3.1.2 copy point from float* to mitk::Contour
// ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
// contourInImageIndexCoordinates->Expand(timestep + 1);
// contourInImageIndexCoordinates->SetClosed(true, timestep);
// Point3D newPoint;
// for (int index = 0; index < cutContour.deleteSize; ++index)
// {
// newPoint[0] = cutContour.deleteCurve[ 2 * index + 0 ] - 0.5;//correction is needed because the
// output of the algorithm is center based
// newPoint[1] = cutContour.deleteCurve[ 2 * index + 1 ] - 0.5;//and we want our contour displayed
// corner based.
// newPoint[2] = 0.0;
// contourInImageIndexCoordinates->AddVertex( newPoint, timestep );
// }
// free(cutContour.traceline);
// free(cutContour.deleteCurve); // perhaps visualize this for fun?
// free(cutContour.onGradient);
// ContourModel::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice(
// m_WorkingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for
// ipSegmentation correction
// FeedbackContourTool::SetFeedbackContour( contourInWorldCoordinates );
// FeedbackContourTool::SetFeedbackContourVisible(true);
// mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
// m_FillFeedbackContour = true;
// }
// else
// {
// m_FillFeedbackContour = false;
// }
// }
// else
// {
// m_FillFeedbackContour = false;
// }
// m_ReferenceSlice = nullptr;
// return true;
}
void mitk::RegionGrowingTool::OnMousePressedOutside(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (positionEvent)
{
// Get geometry and indices
mitk::BaseGeometry::Pointer workingSliceGeometry;
workingSliceGeometry = m_WorkingSlice->GetGeometry();
itk::Index<2> indexInWorkingSlice2D;
indexInWorkingSlice2D[0] = m_SeedPoint[0];
indexInWorkingSlice2D[1] = m_SeedPoint[1];
mitk::BaseGeometry::Pointer referenceSliceGeometry;
referenceSliceGeometry =
m_ReferenceSlice->GetGeometry();
itk::Index<3> indexInReferenceSlice;
itk::Index<2> indexInReferenceSlice2D;
referenceSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), indexInReferenceSlice);
indexInReferenceSlice2D[0] = indexInReferenceSlice[0];
indexInReferenceSlice2D[1] = indexInReferenceSlice[1];
// Get seed neighborhood
ScalarType averageValue(0);
AccessFixedDimensionByItk_3(m_ReferenceSlice, GetNeighborhoodAverage, 2, indexInReferenceSlice2D, &averageValue, 1);
m_SeedValue = averageValue;
MITK_DEBUG << "Seed value is " << m_SeedValue;
// Calculate initial thresholds
AccessFixedDimensionByItk(m_ReferenceSlice, CalculateInitialThresholds, 2);
m_Thresholds[0] = m_InitialThresholds[0];
m_Thresholds[1] = m_InitialThresholds[1];
// Perform region growing
mitk::Image::Pointer resultImage = mitk::Image::New();
AccessFixedDimensionByItk_3(
m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage);
resultImage->SetGeometry(workingSliceGeometry);
// Extract contour
if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1)
{
float isoOffset = 0.33;
mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New();
contourExtractor->SetInput(resultImage);
contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset);
contourExtractor->Update();
ContourModel::Pointer resultContour = ContourModel::New();
resultContour = contourExtractor->GetOutput();
// Show contour
if (resultContour.IsNotNull())
{
ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice(
workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour));
// this is not a beautiful solution, just one that works, check T22412 for details
auto t = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::SetFeedbackContour(0 != t
? ContourModelUtils::MoveZerothContourTimeStep(resultContourWorld, t)
: resultContourWorld);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(m_LastEventSender->GetRenderWindow());
}
}
}
}
void mitk::RegionGrowingTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0,
// i.e. when the user clicked inside the segmentation
if (m_PaintingPixelValue == 0)
{
return;
}
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (m_ReferenceSlice.IsNotNull() && positionEvent)
{
// Get geometry and indices
mitk::BaseGeometry::Pointer workingSliceGeometry;
workingSliceGeometry = m_WorkingSlice->GetGeometry();
itk::Index<2> indexInWorkingSlice2D;
indexInWorkingSlice2D[0] = m_SeedPoint[0];
indexInWorkingSlice2D[1] = m_SeedPoint[1];
m_ScreenYDifference += positionEvent->GetPointerPositionOnScreen()[1] - m_LastScreenPosition[1];
m_ScreenXDifference += positionEvent->GetPointerPositionOnScreen()[0] - m_LastScreenPosition[0];
m_LastScreenPosition = positionEvent->GetPointerPositionOnScreen();
// Moving the mouse up and down adjusts the width of the threshold window,
// moving it left and right shifts the threshold window
m_Thresholds[0] = std::min(m_SeedValue, m_InitialThresholds[0] - (m_ScreenYDifference - m_ScreenXDifference) * m_MouseDistanceScaleFactor);
m_Thresholds[1] = std::max(m_SeedValue, m_InitialThresholds[1] + (m_ScreenYDifference + m_ScreenXDifference) * m_MouseDistanceScaleFactor);
// Do not exceed the pixel type extrema of the reference slice, though
m_Thresholds[0] = std::max(m_ThresholdExtrema[0], m_Thresholds[0]);
m_Thresholds[1] = std::min(m_ThresholdExtrema[1], m_Thresholds[1]);
// Perform region growing again and show the result
mitk::Image::Pointer resultImage = mitk::Image::New();
AccessFixedDimensionByItk_3(
m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage);
resultImage->SetGeometry(workingSliceGeometry);
// Update the contour
if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1)
{
float isoOffset = 0.33;
mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New();
contourExtractor->SetInput(resultImage);
contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset);
contourExtractor->Update();
ContourModel::Pointer resultContour = ContourModel::New();
resultContour = contourExtractor->GetOutput();
// Show contour
if (resultContour.IsNotNull())
{
ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice(
workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour));
// this is not a beautiful solution, just one that works, check T22412 for details
int timestep = positionEvent->GetSender()->GetTimeStep();
if (0 != timestep)
{
int size = resultContourWorld->GetNumberOfVertices(0);
auto resultContourTimeWorld = mitk::ContourModel::New();
resultContourTimeWorld->Expand(timestep + 1);
for (int loop = 0; loop < size; ++loop)
{
resultContourTimeWorld->AddVertex(resultContourWorld->GetVertexAt(loop, 0), timestep);
}
FeedbackContourTool::SetFeedbackContour(resultContourTimeWorld);
}
else
{
FeedbackContourTool::SetFeedbackContour(resultContourWorld);
}
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(positionEvent->GetSender()->GetRenderWindow());
}
}
}
}
void mitk::RegionGrowingTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0,
// i.e. when the user clicked inside the segmentation
if (m_PaintingPixelValue == 0)
{
return;
}
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (m_WorkingSlice.IsNotNull() && m_FillFeedbackContour && positionEvent)
{
// Project contour into working slice
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour;
// this is not a beautiful solution, just one that works, check T22412 for details
int timestep = positionEvent->GetSender()->GetTimeStep();
if (0 != timestep)
{
int size = feedbackContour->GetNumberOfVertices(timestep);
auto feedbackContourTime = mitk::ContourModel::New();
feedbackContourTime->Expand(timestep + 1);
for (int loop = 0; loop < size; ++loop)
{
feedbackContourTime->AddVertex(feedbackContour->GetVertexAt(loop, timestep), 0);
}
projectedContour =
FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, feedbackContourTime, false, false);
}
else
{
projectedContour =
FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, feedbackContour, false, false);
}
// If there is a projected contour, fill it
if (projectedContour.IsNotNull())
{
// Get working data to pass to following method so we don't overwrite locked labels in a LabelSetImage
mitk::DataNode *workingNode(m_ToolManager->GetWorkingData(0));
- mitk::LabelSetImage *labelImage = workingNode != nullptr
+ mitk::LabelSetImage *labelSetImage = workingNode != nullptr
? dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData())
: nullptr;
MITK_DEBUG << "Filling Segmentation";
- if (labelImage != nullptr)
+ if (nullptr != labelSetImage)
{
// m_PaintingPixelValue only decides whether to paint or not
// For LabelSetImages we want to paint with the active label value
- auto activeLabel = labelImage->GetActiveLabel(labelImage->GetActiveLayer())->GetValue();
+ auto activePixelValue = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer())->GetValue();
mitk::ContourModelUtils::FillContourInSlice(projectedContour,
0,
m_WorkingSlice,
- labelImage,
- m_PaintingPixelValue * activeLabel);
+ labelSetImage,
+ m_PaintingPixelValue * activePixelValue);
}
else
{
mitk::ContourModelUtils::FillContourInSlice(projectedContour,
0,
m_WorkingSlice,
m_WorkingSlice,
m_PaintingPixelValue);
}
this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice);
FeedbackContourTool::SetFeedbackContourVisible(false);
}
m_ScreenYDifference = 0;
m_ScreenXDifference = 0;
}
}
diff --git a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp
index 4029a52fa9..79fd3f5bc4 100644
--- a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp
@@ -1,181 +1,181 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSetRegionTool.h"
#include "mitkToolManager.h"
#include "mitkBaseRenderer.h"
#include "mitkImageDataItem.h"
#include "mitkLabelSetImage.h"
#include <mitkITKImageImport.h>
#include <mitkImagePixelReadAccessor.h>
#include <mitkImageToContourModelFilter.h>
#include <itkBinaryFillholeImageFilter.h>
#include <itkConnectedThresholdImageFilter.h>
mitk::SetRegionTool::SetRegionTool(int paintingPixelValue)
: FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue)
{
}
mitk::SetRegionTool::~SetRegionTool()
{
}
void mitk::SetRegionTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Release", OnMouseReleased);
CONNECT_FUNCTION("Move", OnMouseMoved);
}
void mitk::SetRegionTool::Activated()
{
Superclass::Activated();
}
void mitk::SetRegionTool::Deactivated()
{
Superclass::Deactivated();
}
void mitk::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
// 1. Get the working image
Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (workingSlice.IsNull())
return; // can't do anything without the segmentation
// if click was outside the image, don't continue
const BaseGeometry *sliceGeometry = workingSlice->GetGeometry();
itk::Index<3> projectedPointIn2D;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), projectedPointIn2D);
if (!sliceGeometry->IsIndexInside(projectedPointIn2D))
{
MITK_WARN << "Point outside of segmentation slice." << std::endl;
return; // can't use that as a seed point
}
typedef itk::Image<DefaultSegmentationDataType, 2> InputImageType;
typedef InputImageType::IndexType IndexType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// convert world coordinates to image indices
IndexType seedIndex;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), seedIndex);
// perform region growing in desired segmented region
InputImageType::Pointer itkImage = InputImageType::New();
CastToItkImage(workingSlice, itkImage);
regionGrower->SetInput(itkImage);
regionGrower->AddSeed(seedIndex);
InputImageType::PixelType bound = itkImage->GetPixel(seedIndex);
regionGrower->SetLower(bound);
regionGrower->SetUpper(bound);
regionGrower->SetReplaceValue(1);
itk::BinaryFillholeImageFilter<InputImageType>::Pointer fillHolesFilter =
itk::BinaryFillholeImageFilter<InputImageType>::New();
fillHolesFilter->SetInput(regionGrower->GetOutput());
fillHolesFilter->SetForegroundValue(1);
// Store result and preview
mitk::Image::Pointer resultImage = mitk::GrabItkImageMemory(fillHolesFilter->GetOutput());
resultImage->SetGeometry(workingSlice->GetGeometry());
// Get the current working color
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New();
contourextractor->SetInput(resultImage);
contourextractor->Update();
mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput();
auto t = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::SetFeedbackContour(0 != t
? ContourModelUtils::MoveZerothContourTimeStep(awesomeContour, t)
: awesomeContour);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || !planeGeometry)
return;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull())
return;
- auto *labelImage = dynamic_cast<LabelSetImage *>(image);
- int activeColor = 1;
- if (labelImage != nullptr)
+ auto *labelSetImage = dynamic_cast<LabelSetImage *>(image);
+ int activePixelValue = 1;
+ if (nullptr != labelSetImage)
{
- activeColor = labelImage->GetActiveLabel()->GetValue();
+ activePixelValue = labelSetImage->GetActiveLabel()->GetValue();
}
mitk::ContourModelUtils::FillContourInSlice(
- projectedContour, timeStep, slice, image, m_PaintingPixelValue * activeColor);
+ projectedContour, timeStep, slice, image, m_PaintingPixelValue * activePixelValue);
this->WriteBackSegmentationResult(positionEvent, slice);
}
void mitk::SetRegionTool::OnMouseMoved(mitk::StateMachineAction *, mitk::InteractionEvent *)
{
}