cxImportDataTypeWidget.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.

Copyright (c) SINTEF Department of Medical Technology.
All rights reserved.

CustusX is released under a BSD 3-Clause license.

See Lisence.txt (https://github.com/SINTEFMedtek/CustusX/blob/master/License.txt) for details.
=========================================================================*/

#include "cxImportDataTypeWidget.h"
#include <QVBoxLayout>
#include <QHBoxLayout>
#include <QLabel>
#include <QTableWidget>
#include <QHeaderView>
#include <QApplication>
#include <QDesktopWidget>
#include <QCheckBox>
#include <QGroupBox>
#include <QFileInfo>
#include "cxOptionsWidget.h"
#include "cxFileReaderWriterService.h"
#include "cxFileManagerService.h"
#include "cxLogger.h"
#include "cxImage.h"
#include "cxPointMetric.h"
#include "cxLabeledComboBoxWidget.h"
#include "cxVolumeHelpers.h"
#include "cxImageTF3D.h"
#include "cxImageLUT2D.h"
#include "cxViewService.h"
#include "cxImportWidget.h"
#include "cxCustomMetaImage.h"

namespace cx
{

ImportDataTypeWidget::ImportDataTypeWidget(ImportWidget *parent, VisServicesPtr services, std::vector<DataPtr> data, std::vector<DataPtr> &parentCandidates, QString filename) :
        BaseWidget(parent, "ImportDataTypeWidget", "Import"),
        mImportWidget(parent),
        mServices(services),
        mData(data),
        mFilename(filename),
        mParentCandidates(parentCandidates),
        mSelectedIndexInTable(0),
        mImageTypeCombo(NULL),
        mModalityCombo(NULL)

{
        mAnatomicalCoordinateSystems = new QComboBox();
        mAnatomicalCoordinateSystems->addItem("LPS"); //CX
        mAnatomicalCoordinateSystems->addItem("RAS"); //NIfTI

        if(isInputFileInNiftiFormat())
                mAnatomicalCoordinateSystems->setCurrentText("RAS");

        mShouldImportParentTransform = new QComboBox();
        mShouldImportParentTransform->addItem("No");
        mShouldImportParentTransform->addItem("Yes");

        mParentCandidatesCB = new QComboBox();

        mShouldConvertDataToUnsigned = new QCheckBox();
        mShouldConvertDataToUnsigned->setCheckState(Qt::Unchecked);

        mTableWidget = new QTableWidget();
        mTableWidget->setRowCount(0);
        mTableWidget->setColumnCount(4);
        mTableHeader<<"#"<<"Type"<<"Name"<<"Space";
        mTableWidget->setHorizontalHeaderLabels(mTableHeader);
        mTableWidget->horizontalHeader()->setStretchLastSection(true);
        mTableWidget->horizontalHeader()->setSectionResizeMode(QHeaderView::ResizeToContents);
        mTableWidget->verticalHeader()->setVisible(false);
        mTableWidget->setEditTriggers(QAbstractItemView::NoEditTriggers);
        mTableWidget->setSelectionBehavior(QAbstractItemView::SelectRows);
        mTableWidget->setSelectionMode(QAbstractItemView::SingleSelection);
        mTableWidget->setShowGrid(false);
        mTableWidget->setStyleSheet("QTableView {selection-background-color: #ACCEF7;}");
        mTableWidget->setGeometry(QApplication::desktop()->screenGeometry());

        QString type, name;
        for(unsigned i=0; i<mData.size(); ++i)
        {
                if(!mData[i])
                {
                        CX_LOG_WARNING() << "ImportDataTypeWidget::ImportDataTypeWidget: No data";
                        continue;
                }
                type = mData[i]->getType();
                name = mData[i]->getName();
                QString space = mData[i]->getSpace();
                //create point metric groups
                if(type == PointMetric::getTypeName())
                {
                        space = boost::dynamic_pointer_cast<PointMetric>(mData[i])->getSpace().toString();
                        (mPointMetricGroups[space]).push_back(mData[i]);
                }
                //add image or mesh directly to the table
                else
                {
                        int newRowIndex = mTableWidget->rowCount();
                        mTableWidget->setRowCount(newRowIndex+1);
                        mTableWidget->setItem(newRowIndex, 0, new QTableWidgetItem("1"));
                        mTableWidget->setItem(newRowIndex, 1, new QTableWidgetItem(name));
                        mTableWidget->setItem(newRowIndex, 2, new QTableWidgetItem(type));
                        mTableWidget->setItem(newRowIndex, 3, new QTableWidgetItem(space));
                }
                this->createDataSpecificGui(mData[i]);
        }
        this->addPointMetricGroupsToTable();

        //gui
        QVBoxLayout *topLayout = new QVBoxLayout(this);
        this->setLayout(topLayout);

        QFileInfo fileInfo(filename);
        QString title = fileInfo.fileName();

        QGroupBox *groupBox = new QGroupBox(title);

        QGridLayout *gridLayout = new QGridLayout();
        gridLayout->addWidget(new QLabel("For all data in the file: "), 0, 0, 1, 2);
        gridLayout->addWidget(new QLabel("Specify anatomical coordinate system"), 1, 0);
        gridLayout->addWidget(mAnatomicalCoordinateSystems, 1, 1);
        gridLayout->addWidget(new QLabel("Import parents transform?"), 2, 0);
        gridLayout->addWidget(mShouldImportParentTransform, 2, 1);
        gridLayout->addWidget(new QLabel("Set parent"), 3, 0);
        gridLayout->addWidget(mParentCandidatesCB, 3, 1);
        gridLayout->addWidget(new QLabel("Convert data to unsigned?"), 4, 0);
        gridLayout->addWidget(mShouldConvertDataToUnsigned, 4,1);
        gridLayout->addWidget(mTableWidget, 5, 0, 1, 2);
        if(mModalityCombo)
                gridLayout->addWidget(mModalityCombo);
        if(mImageTypeCombo)
                gridLayout->addWidget(mImageTypeCombo);

        groupBox->setLayout(gridLayout);
        topLayout->addWidget(groupBox);

        connect(mImportWidget, &ImportWidget::readyToImport, this, &ImportDataTypeWidget::prepareDataForImport);
        connect(mImportWidget, &ImportWidget::parentCandidatesUpdated, this, &ImportDataTypeWidget::update);
}

ImportDataTypeWidget::~ImportDataTypeWidget()
{
        disconnect(mImportWidget, &ImportWidget::readyToImport, this, &ImportDataTypeWidget::prepareDataForImport);
        disconnect(mImportWidget, &ImportWidget::parentCandidatesUpdated, this, &ImportDataTypeWidget::update);
}


void ImportDataTypeWidget::createDataSpecificGui(DataPtr data)
{
        ImagePtr image = boost::dynamic_pointer_cast<Image>(data);

        if(image)
        {
                mModalityAdapter = StringPropertyDataModality::New(mServices->patient());
                mModalityCombo = new LabeledComboBoxWidget(this, mModalityAdapter);
                mModalityAdapter->setData(image);

                mImageTypeAdapter = StringPropertyImageType::New(mServices->patient());
                mImageTypeCombo = new LabeledComboBoxWidget(this, mImageTypeAdapter);
                mImageTypeAdapter->setData(image);

                if(isInputFileInNiftiFormat()) // NIfTI files are usually MR. Set this as the default
                {
                        mModalityAdapter->setValue(enum2string(imMR));
                        updateImageType();
                }
        }
}

void ImportDataTypeWidget::updateImageType()
{
        // Test code: Trying to use convertToImageSubType on file name to find correct subtype.
        IMAGE_SUBTYPE imageSubType = convertToImageSubType(mFilename);
        mImageTypeAdapter->setValue(enum2string(imageSubType));
}

std::map<QString, QString> ImportDataTypeWidget::getParentCandidateList()
{
        std::map<QString, QString> parentCandidates;
        for(unsigned i=0; i<mParentCandidates.size(); ++i)
        {
                parentCandidates[mParentCandidates[i]->getName()] = mParentCandidates[i]->getUid();
        }

        return parentCandidates;
}

void ImportDataTypeWidget::updateSpaceComboBox(QComboBox *box, QString pointMetricGroupId)
{
        box->clear();
        std::map<QString, QString> parentCandidates = this->getParentCandidateList();
        std::map<QString, QString>::iterator it;
        for(it= parentCandidates.begin(); it != parentCandidates.end(); ++it)
        {
                QVariant id(it->second);
                box->addItem(it->first, id);
        }
        std::vector<DataPtr> pointMetricGroup = mPointMetricGroups[pointMetricGroupId];
        QString currentSpace = pointMetricGroup[0]->getSpace();
        box->setCurrentText(currentSpace);
}

void ImportDataTypeWidget::updateParentCandidatesComboBox()
{
        //remember selection
        QString selectedParentId = (mParentCandidatesCB->itemData(mParentCandidatesCB->currentIndex()).toString());

        mParentCandidatesCB->clear();
        std::map<QString, QString> parentCandidates = this->getParentCandidateList();
        std::map<QString, QString>::iterator it;
        QVariant emptyId("");
        mParentCandidatesCB->addItem("", emptyId);
        int selectedIndex = 0;
        for(it= parentCandidates.begin(); it != parentCandidates.end(); ++it)
        {
                QString idString = it->second;
                QVariant id(idString);
                mParentCandidatesCB->addItem(it->first, id);
                if(selectedParentId.compare(idString, Qt::CaseInsensitive) == 0)
                        selectedIndex = mParentCandidatesCB->count()-1;
        }

        if(selectedIndex != 0)
                mParentCandidatesCB->setCurrentIndex(selectedIndex);

        //TODO parent guess:

        QString parentGuess = this->getInitialGuessForParentFrame();
//      CX_LOG_DEBUG() << "ParentGuess: " << parentGuess;
        mParentCandidatesCB->setCurrentText(parentGuess);


}

void ImportDataTypeWidget::importAllData()
{
        for(unsigned i=0; i<mData.size(); ++i)
        {
                if(mData[i])
                {
                        QString parentId = (mParentCandidatesCB->itemData(mParentCandidatesCB->currentIndex()).toString());
                        mData[i]->get_rMd_History()->setParentSpace(parentId);

                        mServices->patient()->insertData(mData[i]);
                        mServices->view()->autoShowData(mData[i]);
                }
        }
}

void ImportDataTypeWidget::applyParentTransformImport()
{
        CX_LOG_DEBUG() << "applyParentTransformImport()";

        QString parentId = (mParentCandidatesCB->itemData(mParentCandidatesCB->currentIndex()).toString());
        DataPtr parent = mServices->patient()->getData(parentId);

        if(!parent)
        {
                CX_LOG_ERROR() << "Could not find parent data with uid: " << parentId;
                return;
        }

        std::vector<DataPtr>::iterator it = mData.begin();
        for(;it!=mData.end(); ++it)
        {
                DataPtr data = (*it);
                data->get_rMd_History()->setRegistration(parent->get_rMd());
                report("Assigned rMd from data [" + parent->getName() + "] to data [" + data->getName() + "]");
        }

        /*
        if (!mTransformFromParentFrameCheckBox->isChecked())
        return;
        if(!mData)
        return;
        DataPtr parent = mPatientModelService->getData(mData->getParentSpace());
        if (!parent)
        return;
        mData->get_rMd_History()->setRegistration(parent->get_rMd());
        report("Assigned rMd from data [" + parent->getName() + "] to data [" + mData->getName() + "]");
        */
}

void ImportDataTypeWidget::applyConversionLPS()
{
        CX_LOG_DEBUG() << "applyConversionLPS()";

        std::vector<DataPtr>::iterator it = mData.begin();
        for(;it!=mData.end(); ++it)
        {
                DataPtr data = (*it);
                Transform3D sMd = data->get_rMd();
                Transform3D sMr = createTransformFromReferenceToExternal(pcsRAS);
                Transform3D rMd = sMr.inv() * sMd;
                data->get_rMd_History()->setRegistration(rMd);
                report("Nifti import: Converted data " + data->getName() + " from LPS to RAS coordinates.");
        }

        /*
        if (!mNiftiFormatCheckBox->isChecked())
                return;
        if(!mData)
                return;
        Transform3D sMd = mData->get_rMd();
        Transform3D sMr = createTransformFromReferenceToExternal(pcsRAS);
        //  rMd = createTransformRotateZ(M_PI) * rMd;
        Transform3D rMd = sMr.inv() * sMd;
        mData->get_rMd_History()->setRegistration(rMd);
        report("Nifti import: Converted data " + mData->getName() + " from LPS to RAS coordinates.");
        */

}

void ImportDataTypeWidget::applyConversionToUnsigned()
{
        CX_LOG_DEBUG() << "applyConversionToUnsigned()";

        std::vector<DataPtr>::iterator it = mData.begin();
        for(;it!=mData.end(); ++it)
        {
                DataPtr data = (*it);

                ImagePtr image = boost::dynamic_pointer_cast<Image>(data);
                if (!image)
                        return;

                ImagePtr converted = convertImageToUnsigned(mServices->patient(), image);

                image->setVtkImageData(converted->getBaseVtkImageData());

                ImageTF3DPtr TF3D = converted->getTransferFunctions3D()->createCopy();
                ImageLUT2DPtr LUT2D = converted->getLookupTable2D()->createCopy();
                image->setLookupTable2D(LUT2D);
                image->setTransferFunctions3D(TF3D);
                //mServices->patient()->insertData(image);

                DataPtr convertedData = boost::dynamic_pointer_cast<Data>(image);
                (*it) = convertedData;
        }

        /*
        if (!mConvertToUnsignedCheckBox->isChecked())
                return;

        ImagePtr image = boost::dynamic_pointer_cast<Image>(mData);
        if (!image)
                return;

        ImagePtr converted = convertImageToUnsigned(mPatientModelService, image);

        image->setVtkImageData(converted->getBaseVtkImageData());

        ImageTF3DPtr TF3D = converted->getTransferFunctions3D()->createCopy();
        ImageLUT2DPtr LUT2D = converted->getLookupTable2D()->createCopy();
        image->setLookupTable2D(LUT2D);
        image->setTransferFunctions3D(TF3D);
        mPatientModelService->insertData(image);
        */
}

void ImportDataTypeWidget::update()
{
        this->updateParentCandidatesComboBox();

        std::map<QString, QComboBox *>::iterator it;
        for(it=mSpaceCBs.begin(); it != mSpaceCBs.end(); ++it)
        {
                QString id = it->first;
                QComboBox *box = it->second;
                this->updateSpaceComboBox(box,id);
        }
}

void ImportDataTypeWidget::prepareDataForImport()
{
        if(mShouldConvertDataToUnsigned->isChecked())
                this->applyConversionToUnsigned();

        this->importAllData();

        if(mShouldImportParentTransform->currentText() == "Yes")
                this->applyParentTransformImport();
        if(mAnatomicalCoordinateSystems->currentText() != "LPS")
                this->applyConversionLPS();
}

void ImportDataTypeWidget::showEvent(QShowEvent *event)
{
        BaseWidget::showEvent(event);
        this->update();
}

void ImportDataTypeWidget::pointMetricGroupSpaceChanged(int index)
{
        QComboBox *box = qobject_cast<QComboBox*>(QObject::sender());
        QString newSpace = box->currentData().toString();

        QString pointMetricsGroupId;
        std::map<QString, QComboBox *>::iterator it;
        for(it = mSpaceCBs.begin(); it != mSpaceCBs.end(); ++it)
        {
                if(it->second == box)
                        pointMetricsGroupId = it->first;
        }
        std::vector<DataPtr> pointMetricGroup = mPointMetricGroups[pointMetricsGroupId];
        for(unsigned i=0; i<pointMetricGroup.size(); ++i)
        {
                CoordinateSystem cs(csDATA, newSpace);
                boost::dynamic_pointer_cast<PointMetric>(pointMetricGroup[i])->setSpace(cs);
        }
}

QString ImportDataTypeWidget::getInitialGuessForParentFrame()
{
        int candidateScore = 0;
        QString bestCandidate;

        for(unsigned i=0; i < mData.size(); ++i)
        {
                DataPtr data = mData[i];
                std::map<QString, QString> parentCandidates = this->getParentCandidateList();

                std::map<QString, QString>::iterator iter;
                for(iter= parentCandidates.begin(); iter != parentCandidates.end(); ++iter)
                {
                        int similarity = similatiryMeasure(data->getUid(), iter->second);
                        if(similarity > candidateScore && !isSegmentation(iter->second))
                        {
                                candidateScore = similarity;
                                bestCandidate = iter->first;
                        }
                }
        }

        return bestCandidate;
}

int ImportDataTypeWidget::similatiryMeasure(QString current, QString candidate)
{
        QStringList currentList = splitStringIntoSeparateParts(current);
        QStringList candidateList = splitStringIntoSeparateParts(candidate);
        return countEqualListElements(currentList, candidateList);
}

QStringList ImportDataTypeWidget::splitStringIntoSeparateParts(QString current)
{
        current = removeParenthesis(current);

        QStringList list = current.split(".", QString::SkipEmptyParts);
        QStringList list2;
        for (int i = 0; i < list.size(); ++i)
        {
                list2 << list[i].split("_", QString::SkipEmptyParts);
        }
        QStringList currentParts;
        for (int i = 0; i < list2.size(); ++i)
        {
                currentParts << list2[i].split("-", QString::SkipEmptyParts);
        }
        return currentParts;
}

QString ImportDataTypeWidget::removeParenthesis(QString current)
{
                int startParenthesis;
                do
                {
                        startParenthesis = current.indexOf("{");
                        int endParenthesis = current.indexOf("}");
                        current.replace(startParenthesis, endParenthesis-startParenthesis+1, "");
                } while (startParenthesis != -1);
        return current;
}

int ImportDataTypeWidget::countEqualListElements(QStringList first, QStringList second)
{
        int retval = 0;
        int numComparedElements = 0;
        for (int i = 0; i < first.size(); ++i)
        {
                if(excludeElement(first[i]))
                        continue;
                ++numComparedElements;
                for (int j = 0; j < second.size(); ++j)
                {
                        if(first[i].compare(second[j]) == 0)
                        {
                                ++retval;
                                break;//Don't count repeating elements
                        }
                }
        }

        if (retval == numComparedElements)
                return 0;//Don't match equal list
        return retval;
}

bool ImportDataTypeWidget::excludeElement(QString element)
{
        if (isSegmentation(element))
                return true;
        return false;
}

void ImportDataTypeWidget::addPointMetricGroupsToTable()
{
        QString type, name;
        int groupnr = 0;
        std::map<QString, std::vector<DataPtr> >::iterator it = mPointMetricGroups.begin();
        for(; it != mPointMetricGroups.end(); ++it)
        {
                groupnr +=1;

                QString space = it->first;
                std::vector<DataPtr> datas = it->second;
                DataPtr data = datas[0];
                if(datas.empty() || !data)
                {
                        continue;
                }

                QComboBox *spaceCB = new QComboBox();
                mSpaceCBs[space] = spaceCB;
                connect(spaceCB, SIGNAL(currentIndexChanged(int)), this, SLOT(pointMetricGroupSpaceChanged(int)));
                this->updateSpaceComboBox(spaceCB, space);

                type = data->getType();
                name = "Point metric group "+QString::number(groupnr);

                int newRowIndex = mTableWidget->rowCount();
                mTableWidget->setRowCount(newRowIndex+1);
                mTableWidget->setItem(newRowIndex, 0, new QTableWidgetItem(QString::number(datas.size())));
                mTableWidget->setItem(newRowIndex, 1, new QTableWidgetItem(name));
                mTableWidget->setItem(newRowIndex, 2, new QTableWidgetItem(type));
                mTableWidget->setCellWidget(newRowIndex, 3, spaceCB);
        }
}

bool ImportDataTypeWidget::isInputFileInNiftiFormat()
{
        if(mFilename.endsWith(".nii", Qt::CaseInsensitive))
                return true;
        return false;
}

bool ImportDataTypeWidget::isSegmentation(QString filename)
{
        if(filename.contains("label", Qt::CaseInsensitive))
                return true;
        if(filename.contains("seg", Qt::CaseInsensitive))
                return true;
        return false;
}

}