The expiration time for new job artifacts in CI/CD pipelines is now 30 days (GitLab default). Previously generated artifacts in already completed jobs will not be affected by the change. The latest artifacts for all jobs in the latest successful pipelines will be kept. More information: https://gitlab.lrz.de/help/user/admin_area/settings/continuous_integration.html#default-artifacts-expiration

Commit da01f3cb authored by schultezub's avatar schultezub
Browse files

Introducing very simple VTK image reader

git-svn-id: https://camplinux.in.tum.de/svn/campvis/trunk@427 bb408c1c-ae56-11e1-83d9-df6b3e0c105e
parent 1a816b77
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// If not explicitly stated otherwise: Copyright (C) 2012, all rights reserved,
// Christian Schulte zu Berge <christian.szb@in.tum.de>
// Chair for Computer Aided Medical Procedures
// Technische Universitt Mnchen
// Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// The licensing of this softare is not yet resolved. Until then, redistribution in source or
// binary forms outside the CAMP chair is not permitted, unless explicitly stated in legal form.
// However, the names of the original authors and the above copyright notice must retain in its
// original state in any case.
//
// Legal disclaimer provided by the BSD license:
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
// AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
// ================================================================================================
#include "vtkimagereader.h"
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include "tgt/filesystem.h"
#include "core/datastructures/imagedata.h"
#include "core/datastructures/imagerepresentationdisk.h"
#include "core/datastructures/genericimagerepresentationlocal.h"
#include "core/tools/stringutils.h"
/*
* Full format specification at http://www.vtk.org/VTK/img/file-formats.pdf
*/
namespace campvis {
const std::string VtkImageReader::loggerCat_ = "CAMPVis.modules.io.VtkImageReader";
VtkImageReader::VtkImageReader()
: AbstractProcessor()
, p_url("url", "Image URL", "")
, p_targetImageID("targetImageName", "Target Image ID", "VtkImageReader.output", DataNameProperty::WRITE)
, p_imageOffset("ImageOffset", "Image Offset in mm", tgt::vec3(0.f), tgt::vec3(-10000.f), tgt::vec3(10000.f))
, p_voxelSize("VoxelSize", "Voxel Size in mm", tgt::vec3(1.f), tgt::vec3(-100.f), tgt::vec3(100.f))
{
addProperty(&p_url);
addProperty(&p_targetImageID);
addProperty(&p_imageOffset);
addProperty(&p_voxelSize);
}
VtkImageReader::~VtkImageReader() {
}
std::string getTrimmedLine(std::ifstream& file, char delim = '\n') {
std::string toReturn;
std::getline(file, toReturn, delim);
return StringUtils::trim(toReturn);
}
void VtkImageReader::process(DataContainer& data) {
try {
std::ifstream file(p_url.getValue(), std::ifstream::in);
if (!file.is_open() || file.bad())
throw tgt::FileException("Could not open file " + p_url.getValue() + " for reading.", p_url.getValue());
std::string curLine = getTrimmedLine(file);
if (curLine.find("# vtk DataFile Version") != 0)
throw tgt::FileException("Unknown identifier in vtk file.", p_url.getValue());
// init optional parameters with sane default values
bool binary = false;
std::string url;
size_t dimensionality = 3;
tgt::svec3 size(0U);
tgt::vec3 voxelSize(1.f);
tgt::vec3 imageOffset(0.f);
// next line is the header - contains only unimportant data
curLine = getTrimmedLine(file);
// this line is the format
curLine = StringUtils::lowercase(getTrimmedLine(file));
if (curLine == "ascii")
binary = false;
else if (curLine == "binary")
binary = true;
else
throw tgt::FileException("Unsupported format in vtk file - expected binary or ascii.", p_url.getValue());
// now comes the dataset structure
curLine = StringUtils::lowercase(getTrimmedLine(file));
std::vector<std::string> splitted = StringUtils::split(curLine, " ");
if (splitted.size() != 2 || splitted[0] != "dataset" || splitted[1] != "structured_points")
throw tgt::FileException("Unsupported dataset structure in vtk file - expected \"DATASET STRUCTURED_POINTS\".", p_url.getValue());
// now comes dimensions, spacing and origin:
for (size_t i = 0; i < 3; ++i) {
std::stringstream ss(StringUtils::lowercase(getTrimmedLine(file)));
ss >> curLine;
if (curLine == "dimensions") {
ss >> size.x >> size.y >> size.z;
if (size.z == 1)
dimensionality = 2;
if (size.y == 1)
dimensionality = 1;
}
else if (curLine == "spacing") {
ss >> voxelSize.x >> voxelSize.y >> voxelSize.z;
}
else if (curLine == "origin") {
ss >> imageOffset.x >> imageOffset.y >> imageOffset.z;
}
else {
throw tgt::FileException("Unsupported dataset structure field '" + curLine + "' in vtk file.", p_url.getValue());
}
}
// now come the dataset attributes "POINT_DATA ..."
curLine = StringUtils::lowercase(getTrimmedLine(file));
splitted = StringUtils::split(curLine, " ");
if (splitted.size() != 2 || splitted[0] != "point_data")
throw tgt::FileException("Unsupported dataset attribute '" + splitted[0] + "' in vtk file - expected \"POINT_DATA n\".", p_url.getValue());
size_t numPoints = StringUtils::fromString<size_t>(splitted[1]);
if (numPoints < tgt::hmul(size))
throw tgt::FileException("Number of points in dataset (" + splitted[0] + ") doesn't match dimensions: " + StringUtils::toString(size), p_url.getValue());
// now comes the data description block "FIELD ..."
curLine = StringUtils::lowercase(getTrimmedLine(file));
splitted = StringUtils::split(curLine, " ");
if (splitted.size() != 3 || splitted[0] != "field")
throw tgt::FileException("Unsupported dataset attribute '" + splitted[0] + "' in vtk file - expected \"FIELD ...\".", p_url.getValue());
size_t numArrays = StringUtils::fromString<size_t>(splitted[2]);
if (numArrays != 1)
throw tgt::FileException("Multiple arrays in data set currently not supported - too lazy...", p_url.getValue());
curLine = StringUtils::lowercase(getTrimmedLine(file));
splitted = StringUtils::split(curLine, " ");
size_t numTuples = StringUtils::fromString<size_t>(splitted[1]);
size_t numComponents = StringUtils::fromString<size_t>(splitted[2]);
if (numTuples * numComponents != numPoints)
throw tgt::FileException("Number of points in dataset doesn't match dimensions of data field", p_url.getValue());
if (! binary) {
ImageData* image = new ImageData(dimensionality, size, 1);
ImageRepresentationLocal* rep = 0;
#define DISPATCH_PARSING(VTK_TYPE, C_TYPE, TMP_TYPE) \
do { \
if (splitted[3] == VTK_TYPE) { \
C_TYPE* data = new C_TYPE[numPoints]; \
TMP_TYPE tmp; \
for (size_t i = 0; i < numPoints && file.good(); ++i) { \
file >> tmp; \
data[i] = static_cast<C_TYPE>(tmp); \
} \
rep = new GenericImageRepresentationLocal<C_TYPE, 1>(image, data); \
} \
} while (0)
DISPATCH_PARSING("unsigned_char", uint8_t, uint16_t);
DISPATCH_PARSING("char", int8_t, int16_t);
DISPATCH_PARSING("unsigned_short", uint16_t, uint16_t);
DISPATCH_PARSING("short", int16_t, int16_t);
DISPATCH_PARSING("unsigned_int", uint32_t, uint32_t);
DISPATCH_PARSING("int", int32_t, int32_t);
DISPATCH_PARSING("float", float, float);
if (rep != 0) {
// all parsing done - lets create the image:
image->setMappingInformation(ImageMappingInformation(size, imageOffset + p_imageOffset.getValue(), voxelSize + p_voxelSize.getValue()));
data.addData(p_targetImageID.getValue(), image);
p_targetImageID.issueWrite();
}
else {
throw tgt::FileException("Error while parsing the data.", p_url.getValue());
}
}
else {
throw tgt::FileException("Binary data format currently unsupported.", p_url.getValue());
}
}
catch (tgt::Exception& e) {
LERROR("Error while parsing VTK file: " << e.what());
return;
}
catch (std::exception& e) {
LERROR("Error while parsing VTK file: " << e.what());
return;
}
_invalidationLevel.setValid();
}
}
\ No newline at end of file
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// If not explicitly stated otherwise: Copyright (C) 2012, all rights reserved,
// Christian Schulte zu Berge <christian.szb@in.tum.de>
// Chair for Computer Aided Medical Procedures
// Technische Universität München
// Boltzmannstr. 3, 85748 Garching b. München, Germany
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// The licensing of this softare is not yet resolved. Until then, redistribution in source or
// binary forms outside the CAMP chair is not permitted, unless explicitly stated in legal form.
// However, the names of the original authors and the above copyright notice must retain in its
// original state in any case.
//
// Legal disclaimer provided by the BSD license:
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
// AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
// ================================================================================================
#ifndef VTKIMAGEREADER_H__
#define VTKIMAGEREADER_H__
#include <string>
#include "core/pipeline/abstractprocessor.h"
#include "core/properties/datanameproperty.h"
#include "core/properties/numericproperty.h"
namespace campvis {
/**
* Reads a VTK image file into the pipeline.
*
* \note Full format specification at http://www.vtk.org/VTK/img/file-formats.pdf
*/
class VtkImageReader : public AbstractProcessor {
public:
/**
* Constructs a new VtkImageReader Processor
**/
VtkImageReader();
/**
* Destructor
**/
virtual ~VtkImageReader();
/**
* Reads the MHD file into an ImageRepresentationDisk representation
* \param data DataContainer to work on
*/
virtual void process(DataContainer& data);
/// \see AbstractProcessor::getName()
virtual const std::string getName() const { return "VtkImageReader"; };
/// \see AbstractProcessor::getDescription()
virtual const std::string getDescription() const { return "Reads an MHD image into the pipeline."; };
StringProperty p_url; ///< URL for file to read
DataNameProperty p_targetImageID; ///< image ID for read image
Vec3Property p_imageOffset; ///< Image Offset in mm
Vec3Property p_voxelSize; ///< Voxel Size in mm
protected:
static const std::string loggerCat_;
};
}
#endif // VTKIMAGEREADER_H__
\ No newline at end of file
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