VtkRaster.cpp

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#include "VtkRaster.h"
 
#include <vtkBMPReader.h>
#include <vtkImageData.h>
#include <vtkImageImport.h>
#include <vtkImageReader2.h>
#include <vtkJPEGReader.h>
#include <vtkPNGReader.h>
#include <vtkTIFFReader.h>
 
#include <QFileInfo>
#include <algorithm>
#include <cmath>
#include <limits>
 
#ifdef GEOTIFF_FOUND
#include <geo_tiffp.h>
#include <xtiffio.h>
#endif
 
#include <memory>
 
#include "Applications/FileIO/AsciiRasterInterface.h"
#include "BaseLib/FileTools.h"
#include "BaseLib/Logging.h"
#include "BaseLib/StringTools.h"
#include "GeoLib/Raster.h"
 
vtkImageAlgorithm* VtkRaster::loadImage(const std::string& fileName)
{
    QFileInfo fileInfo(QString::fromStdString(fileName));
 
    std::unique_ptr<GeoLib::Raster> raster(nullptr);
    if (fileInfo.suffix().toLower() == "asc")
    {
        raster.reset(
            FileIO::AsciiRasterInterface::getRasterFromASCFile(fileName));
    }
    else if (fileInfo.suffix().toLower() == "grd")
    {
        raster.reset(
            FileIO::AsciiRasterInterface::getRasterFromSurferFile(fileName));
    }
    if (raster)
    {
        return VtkRaster::loadImageFromArray(raster->begin(),
                                             raster->getHeader());
    }
    if ((fileInfo.suffix().toLower() == "tif") ||
        (fileInfo.suffix().toLower() == "tiff"))
    {
#ifdef GEOTIFF_FOUND
        return loadImageFromTIFF(fileName);
#else
        ERR("VtkRaster::loadImage(): GeoTiff file format not supported in this "
            "version! Trying to parse as Tiff-file.");
        return loadImageFromFile(fileName);
#endif
    }
 
    return loadImageFromFile(fileName);
}
vtkImageImport* VtkRaster::loadImageFromArray(double const* const data_array,
                                              GeoLib::RasterHeader header)
{
    const unsigned length = header.n_rows * header.n_cols * header.n_depth;
    auto* data = new float[length * 2];
    float max_val =
        static_cast<float>(*std::max_element(data_array, data_array + length));
    for (unsigned j = 0; j < length; ++j)
    {
        data[j * 2] = static_cast<float>(data_array[j]);
        if (fabs(data[j * 2] - header.no_data) <
            std::numeric_limits<double>::epsilon())
        {
            data[j * 2] = max_val;
            data[j * 2 + 1] = 0;
        }
        else
        {
            data[j * 2 + 1] = max_val;
        }
    }
 
    vtkImageImport* image = vtkImageImport::New();
    image->SetDataSpacing(header.cell_size, header.cell_size, header.cell_size);
    image->SetDataOrigin(header.origin[0] + (header.cell_size / 2.0),
                         header.origin[1] + (header.cell_size / 2.0),
                         0);  // translate whole mesh by half a pixel in x and y
    image->SetWholeExtent(0, header.n_cols - 1, 0, header.n_rows - 1, 0,
                          header.n_depth - 1);
    image->SetDataExtent(0, header.n_cols - 1, 0, header.n_rows - 1, 0,
                         header.n_depth - 1);
    image->SetDataExtentToWholeExtent();
    image->SetDataScalarTypeToFloat();
    image->SetNumberOfScalarComponents(2);
    image->SetImportVoidPointer(data, 0);
    image->Update();
 
    return image;
}
 
#ifdef GEOTIFF_FOUND
vtkImageAlgorithm* VtkRaster::loadImageFromTIFF(const std::string& fileName)
{
    TIFF* tiff = XTIFFOpen(fileName.c_str(), "r");
 
    if (tiff)
    {
        GTIF* geoTiff = GTIFNew(tiff);
 
        int version[3];
        int count(0);
        GTIFDirectoryInfo(geoTiff, version, &count);
 
        if (count == 0)
            WARN("VtkRaster::loadImageFromTIFF - file is not georeferenced.");
 
        if (geoTiff)
        {
            double x0 = 0.0;
            double y0 = 0.0;
            double cellsize = 1.0;
            int imgWidth = 0;
            int imgHeight = 0;
            int nImages = 0;
            int pntCount = 0;
            double* pnts = nullptr;
 
            // get actual number of images in the tiff file
            do
            {
                ++nImages;
            } while (TIFFReadDirectory(tiff));
            if (nImages > 1)
                INFO(
                    "VtkRaster::loadImageFromTIFF() - File contains {:d} "
                    "images. This method is not tested for this case.",
                    nImages);
 
            // get image size
            TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &imgWidth);
            TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &imgHeight);
 
            // get cellsize
            // Note: GeoTiff allows anisotropic pixels. This is not supported
            // here and equilateral pixels are assumed.
            if (TIFFGetField(tiff, GTIFF_PIXELSCALE, &pntCount, &pnts))
            {
                if (pnts[0] != pnts[1])
                    WARN(
                        "VtkRaster::loadImageFromTIFF(): Original raster data "
                        "has anisotrop pixel size!");
                cellsize = pnts[0];
            }
 
            // get upper left point / origin
            if (TIFFGetField(tiff, GTIFF_TIEPOINTS, &pntCount, &pnts))
            {
                x0 = pnts[3];
                y0 = pnts[4] -
                     (imgHeight * cellsize);  // the origin should be the lower
                                              // left corner of the img
            }
 
            // read pixel values
            auto* pixVal = static_cast<uint32*>(
                _TIFFmalloc(imgWidth * imgHeight * sizeof(uint32)));
            if ((imgWidth > 0) && (imgHeight > 0))
            {
                if (!TIFFReadRGBAImage(tiff, imgWidth, imgHeight, pixVal, 0))
                {
                    ERR("VtkRaster::loadImageFromTIFF(): reading GeoTIFF "
                        "file.");
                    _TIFFfree(pixVal);
                    GTIFFree(geoTiff);
                    XTIFFClose(tiff);
                    return nullptr;
                }
            }
 
            // check for colormap
            uint16 photometric;
            TIFFGetField(tiff, TIFFTAG_PHOTOMETRIC, &photometric);
            // read colormap
            uint16 *cmap_red = nullptr, *cmap_green = nullptr,
                   *cmap_blue = nullptr;
            int colormap_used = TIFFGetField(tiff, TIFFTAG_COLORMAP, &cmap_red,
                                             &cmap_green, &cmap_blue);
 
            auto* data = new float[imgWidth * imgHeight * 4];
            auto* pxl(new int[4]);
            for (int j = 0; j < imgHeight; ++j)
            {
                int lineindex = j * imgWidth;
                for (int i = 0; i < imgWidth; ++i)
                {  // scale intensities and set nodata values to white (i.e. the
                   // background colour)
                    unsigned pxl_idx(lineindex + i);
                    unsigned pos = 4 * (pxl_idx);
                    if (photometric == 1 && colormap_used == 1)
                    {
                        int idx = TIFFGetR(pixVal[pxl_idx]);
                        data[pos] = static_cast<float>(cmap_red[idx] >> 8);
                        data[pos + 1] =
                            static_cast<float>(cmap_green[idx] >> 8);
                        data[pos + 2] = static_cast<float>(cmap_blue[idx] >> 8);
                        data[pos + 3] = 1;
                    }
                    else
                    {
                        data[pos] =
                            static_cast<float>(TIFFGetR(pixVal[pxl_idx]));
                        data[pos + 1] =
                            static_cast<float>(TIFFGetG(pixVal[pxl_idx]));
                        data[pos + 2] =
                            static_cast<float>(TIFFGetB(pixVal[pxl_idx]));
                        data[pos + 3] =
                            static_cast<float>(TIFFGetA(pixVal[pxl_idx]));
                    }
                }
            }
            delete[] pxl;
 
            // set transparency values according to maximum pixel value
            if (photometric == 1)
            {
                float max_val(0);
                unsigned nPixels = 4 * imgWidth * imgHeight;
                for (unsigned j = 0; j < nPixels; ++j)
                {
                    if (data[j] > max_val)
                    {
                        max_val = data[j];
                    }
                }
 
                for (unsigned j = 0; j < nPixels; j += 4)
                {
                    data[j + 3] = max_val;
                }
            }
 
            vtkImageImport* image = vtkImageImport::New();
            image->SetDataOrigin(x0, y0, 0);
            image->SetDataSpacing(cellsize, cellsize, cellsize);
            image->SetWholeExtent(0, imgWidth - 1, 0, imgHeight - 1, 0, 0);
            image->SetDataExtent(0, imgWidth - 1, 0, imgHeight - 1, 0, 0);
            image->SetDataExtentToWholeExtent();
            image->SetDataScalarTypeToFloat();
            image->SetNumberOfScalarComponents(4);
            image->SetImportVoidPointer(data, 0);
            image->Update();
 
            _TIFFfree(pixVal);
            GTIFFree(geoTiff);
            XTIFFClose(tiff);
            return image;
        }
 
        XTIFFClose(tiff);
        ERR("VtkRaster::loadImageFromTIFF() - File not recognised as "
            "GeoTIFF-Image.");
        return nullptr;
    }
 
    ERR("VtkRaster::loadImageFromTIFF() - File not recognised as TIFF-Image.");
    return nullptr;
}
#endif
 
vtkImageReader2* VtkRaster::loadImageFromFile(const std::string& fileName)
{
    QString file_name(QString::fromStdString(fileName));
    QFileInfo fi(file_name);
    vtkImageReader2* image(nullptr);
 
    if (fi.suffix().toLower() == "png")
    {
        image = vtkPNGReader::New();
    }
    else if ((fi.suffix().toLower() == "tif") ||
             (fi.suffix().toLower() == "tiff"))
    {
        image = vtkTIFFReader::New();
    }
    else if ((fi.suffix().toLower() == "jpg") ||
             (fi.suffix().toLower() == "jpeg"))
    {
        image = vtkJPEGReader::New();
    }
    else if (fi.suffix().toLower() == "bmp")
    {
        image = vtkBMPReader::New();
    }
    else
    {
        ERR("VtkRaster::readImageFromFile(): File format not supported, please "
            "convert to BMP, JPG, PNG or TIFF.");
        return nullptr;
    }
 
    image->SetFileName(fileName.c_str());
    image->GetOutput()->AllocateScalars(VTK_FLOAT, 1);
    image->Update();
    readWorldFile(fileName, image);
    return image;
}
 
std::string VtkRaster::findWorldFile(std::string const& filename)
{
    std::string const no_ext = BaseLib::dropFileExtension(filename);
 
    constexpr std::array supported_extensions = {
        ".pgw",  ".pngw", ".pgwx", ".jgw",  ".jpgw", ".jgwx", ".tfw",
        ".tifw", ".tfwx", ".bpw",  ".bmpw", ".bpwx", ".wld"};
 
    auto const res =
        std::find_if(supported_extensions.begin(), supported_extensions.end(),
                     [&no_ext](auto const& ext) -> bool
                     { return BaseLib::IsFileExisting(no_ext + ext); });
    if (res != supported_extensions.end())
    {
        return no_ext + *res;
    }
 
    // no world file found
    return {};
}
 
bool VtkRaster::readWorldFile(std::string const& filename,
                              vtkImageReader2* image)
{
    std::string const world_file = findWorldFile(filename);
    if (world_file.empty())
    {
        WARN("No world file found. Image is not georeferenced.");
        return false;
    }
 
    std::ifstream in(world_file.c_str());
    if (!in.is_open())
    {
        ERR("VtkRaster::readWorldFile(): Could not open file {:s}.", filename);
        return false;
    }
 
    std::string line;
    // x-scaling
    if (!std::getline(in, line))
    {
        return false;
    }
    double const delta_x = BaseLib::str2number<double>(line);
    // 2x rotation (ignored)
    if (!(std::getline(in, line) && std::getline(in, line)))
    {
        return false;
    }
    // negative y-scaling
    if (!std::getline(in, line))
    {
        return false;
    }
    double const delta_y = BaseLib::str2number<double>(line);
    if (delta_x != -delta_y)
        WARN(
            "Anisotropic pixel size detected ({:f} vs {:f}). An isotropic "
            "spacing of {:f} is assumed, be aware results may be wrong.",
            delta_x, delta_y, delta_x);
    // x-translation
    if (!std::getline(in, line))
    {
        return false;
    }
    double const x0 = BaseLib::str2number<double>(line);
    // y-translation
    if (!std::getline(in, line))
    {
        return false;
    }
    double const y0 = BaseLib::str2number<double>(line);
 
    int extent[3];
    image->GetOutput()->GetDimensions(extent);
    image->SetDataSpacing(delta_x, delta_x, delta_x);
    // for GIS the origin is on the lower left, for VTK it is on the upper left
    double const vtk_y0 = y0 + (extent[1] * delta_y);
    image->SetDataOrigin(x0, vtk_y0, 0);
    return true;
}