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/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2025 Univ. Grenoble Alpes, CNRS, Grenoble INP - UGA, TIMC, 38000 Grenoble, France
*
* Visit http://camitk.imag.fr for more information
*
* This file is part of CamiTK.
*
* CamiTK is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License version 3
* only, as published by the Free Software Foundation.
*
* CamiTK is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License version 3 for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* version 3 along with CamiTK. If not, see <http://www.gnu.org/licenses/>.
*
* $CAMITK_LICENCE_END$
****************************************************************************/
#include "VtkImageComponent.h"
#include <ImageComponent.h>
#include <Log.h>
//-- Qt
#include <QFileInfo>
#include <QRegularExpression>
#include <QTextStream>
//-- Vtk
// disable warning generated by clang about the surrounded headers
#include <CamiTKDisableWarnings>
// vtk image readers
#include <vtkImageReader2.h>
#include <vtkJPEGReader.h>
#include <vtkPNGReader.h>
#include <vtkTIFFReader.h>
#include <vtkBMPReader.h>
#include <vtkPNMReader.h>
#include <vtkMetaImageReader.h>
#include <CamiTKReEnableWarnings>
#include <vtkImageData.h>
#include <vtkImageFlip.h>
#include <vtkInformation.h>
using namespace camitk;
// -------------------- constructor --------------------
VtkImageComponent::VtkImageComponent(const QString& fileName)
: ImageComponent(fileName, QFileInfo(fileName).baseName()) {
readImageData(fileName);
}
// -------------------- readImageData --------------------
void VtkImageComponent::readImageData(const QString& filename) {
if (!filename.isNull()) {
try {
// Reader and image variables
vtkSmartPointer<vtkImageReader2> reader;
vtkSmartPointer<vtkImageData> image = nullptr;
// filename extension
QString fileExt = QFileInfo(filename).suffix();
// Reader initialization, depending on file extension
if (QString::compare(fileExt, "jpg", Qt::CaseInsensitive) == 0) {
reader = vtkSmartPointer<vtkJPEGReader>::New();
}
else if (QString::compare(fileExt, "png", Qt::CaseInsensitive) == 0) {
reader = vtkSmartPointer<vtkPNGReader>::New();
}
else if ((QString::compare(fileExt, "tiff", Qt::CaseInsensitive) == 0) ||
(QString::compare(fileExt, "tif", Qt::CaseInsensitive) == 0)) {
reader = vtkSmartPointer<vtkTIFFReader>::New();
}
else if (QString::compare(fileExt, "bmp", Qt::CaseInsensitive) == 0) {
reader = vtkSmartPointer<vtkBMPReader>::New();
}
else if ((QString::compare(fileExt, "pbm", Qt::CaseInsensitive) == 0) ||
(QString::compare(fileExt, "pgm", Qt::CaseInsensitive) == 0) ||
(QString::compare(fileExt, "ppm", Qt::CaseInsensitive) == 0)) {
reader = vtkSmartPointer<vtkPNMReader>::New();
}
else if ((QString::compare(fileExt, "mhd", Qt::CaseInsensitive) == 0) ||
(QString::compare(fileExt, "mha", Qt::CaseInsensitive) == 0)) {
reader = vtkSmartPointer<vtkMetaImageReader>::New();
}
else {
throw AbortException("File format " + fileExt.toStdString() + " not supported yet.");
}
std::string stdFilename = QFileInfo(filename).absoluteFilePath().toStdString();
if (reader) {
reader->SetFileName(stdFilename.c_str());
try {
reader->Update();
}
catch (...) {
throw AbortException("VTK was unable to read file " + stdFilename);
}
image = reader->GetOutput();
}
// Get the image orientation & rotation when possible
ImageOrientationHelper::PossibleImageOrientations orientation = ImageOrientationHelper::RAI;
vtkSmartPointer<vtkMatrix4x4> rotationMatrix;
if (vtkSmartPointer<vtkMetaImageReader> metaImageReader = vtkMetaImageReader::SafeDownCast(reader)) {
orientation = ImageOrientationHelper::getOrientationAsEnum(QString(metaImageReader->GetAnatomicalOrientation()));
rotationMatrix = readMetaImageTransformMatrix(filename);
}
// set the image data, orientation and rotation matrix
// note : the orientation is always displayed using RAI inside CamiTK
// therefore the transformation from orientation to RAI is applied in setImageData
// Inside the ImageComponent, initialImageDataTransform stores the transformation : [ translation ] * [ orientation -> RAI ]
setImageData(image, false, orientation, rotationMatrix);
image = nullptr;
reader = nullptr;
}
catch (const AbortException& e) {
throw (e);
}
}
}
// -------------------- readMetaImageTransformMatrix --------------------
vtkSmartPointer<vtkMatrix4x4> VtkImageComponent::readMetaImageTransformMatrix(const QString& fileName) {
QFile file(fileName);
if (!file.open(QIODevice::ReadOnly | QIODevice::Text)) {
CAMITK_ERROR(tr("Cannot open file \"%1\" to read TransformMatrix tag from image").arg(fileName))
return nullptr;
}
QRegularExpression regExp = QRegularExpression("TransformMatrix = ([-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?[ |\\n])+");
QTextStream in(&file);
QString line = in.readLine();
while (!line.isNull()) {
// Find lind feature TransformMatrix tag information
if (line.contains(regExp)) { // found it !
// retrieve information
QStringList values = line.split(" ");
int nDim;
if (values.size() >= 9 + 2) {
// if the read matrix is 9 elements ( + "TransformMatrix" + "=") or more
// manage it as a 3D matrix
nDim = 3;
}
else {
// else manage it as a 2D matrix
nDim = 2;
}
// According to https://itk.org/Wiki/MetaIO/Documentation#Associated_transformations
// "matrix that is serialized in a column-major format" -> fill column by column
vtkSmartPointer<vtkMatrix4x4> rotationMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
for (int j = 0; j < nDim; j++) { // lines
for (int i = 0; i < nDim; i++) { // columns
rotationMatrix->SetElement(i, j, values.at(j * nDim + i + 2).toDouble());
}
}
file.close();
return rotationMatrix;
}
line = in.readLine();
}
file.close(); // close the file handle.
return nullptr;
}
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