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// ************************************************************************************************
//
// BornAgain: simulate and fit reflection and scattering
//
//! @file Device/IO/ReadWriteTiff.cpp
//! @brief Implements functions readTiff, writeTiff.
//!
//! @homepage http://www.bornagainproject.org
//! @license GNU General Public License v3 or higher (see COPYING)
//! @copyright Forschungszentrum Jülich GmbH 2018
//! @authors Scientific Computing Group at MLZ (see CITATION, AUTHORS)
//
// ************************************************************************************************
#ifdef BA_TIFF_SUPPORT
#include "Device/IO/ReadWriteTiff.h"
#include "Base/Axis/Frame.h"
#include "Base/Axis/MakeScale.h"
#include "Base/Axis/Scale.h"
#include "Base/Util/Assert.h"
#include "Base/Util/SysUtil.h"
#include "Device/Data/Datafield.h"
#include <cstring> // memcpy
#include <memory>
#include <sstream>
#include <tiffio.h>
#include <tiffio.hxx>
namespace {
const std::string ref_to_doc =
"\n\nThe TIFF format requirements can be found in the web documentation.";
} // namespace
Datafield Util::RW::readTiff(std::istream& input_stream)
{
// Update webdoc page about tiff requirements if they are changed.
TIFF* tiffstream = TIFFStreamOpen("MemTIFF", &input_stream);
if (!tiffstream)
throw std::runtime_error("Cannot open the TIFF file" + ref_to_doc);
//... Read header.
std::ostringstream message;
message << "Cannot read TIFF file:" << std::endl;
uint32_t w, h;
if (!TIFFGetField(tiffstream, TIFFTAG_IMAGEWIDTH, &w)
|| !TIFFGetField(tiffstream, TIFFTAG_IMAGELENGTH, &h)) {
message << "missing width/height in header" << ref_to_doc << std::endl;
throw std::runtime_error(message.str());
}
// BitsPerSample defaults to 1 according to the TIFF spec.
uint16_t bitsPerSample;
if (!TIFFGetField(tiffstream, TIFFTAG_BITSPERSAMPLE, &bitsPerSample))
bitsPerSample = 1;
if (8 != bitsPerSample && 16 != bitsPerSample && 32 != bitsPerSample) {
message << " TIFFTAG_BITSPERSAMPLE: " << bitsPerSample << std::endl
<< "Only 8, 16 or 32 bits per sample are allowed." << ref_to_doc << std::endl;
throw std::runtime_error(message.str());
}
// they may be e.g. grayscale with 2 samples per pixel
uint16_t samplesPerPixel;
if (!TIFFGetField(tiffstream, TIFFTAG_SAMPLESPERPIXEL, &samplesPerPixel))
samplesPerPixel = 1;
if (samplesPerPixel != 1) {
message << " TIFFTAG_SAMPLESPERPIXEL: " << samplesPerPixel << std::endl
<< "Only 1 sample per pixel (channel) is allowed." << ref_to_doc << std::endl;
throw std::runtime_error(message.str());
}
uint16_t sampleFormat;
if (!TIFFGetField(tiffstream, TIFFTAG_SAMPLEFORMAT, &sampleFormat))
sampleFormat = 1;
switch (sampleFormat) {
case 1: // unsigned int
case 2: // signed int
break;
case 3: // IEEE float
if (32 != bitsPerSample) {
message
<< " TIFFTAG_BITSPERSAMPLE: " << bitsPerSample << std::endl
<< " TIFFTAG_SAMPLEFORMAT: " << sampleFormat << std::endl
<< "Only 32 bits per sample are allowed for IEEE float format (sample format = 3)."
<< ref_to_doc << std::endl;
throw std::runtime_error(message.str());
}
break;
default:
message << " TIFFTAG_SAMPLEFORMAT: " << sampleFormat << std::endl
<< "Only value 1, 2 or 3 is allowed." << ref_to_doc << std::endl;
throw std::runtime_error(message.str());
}
//... Read data.
ASSERT(0 == bitsPerSample % 8);
uint16_t bytesPerSample = bitsPerSample / 8;
tmsize_t buf_size = TIFFScanlineSize(tiffstream);
tmsize_t expected_size = bytesPerSample * w;
if (buf_size != expected_size)
throw std::runtime_error("Cannot read TIFF file: wrong scanline size" + ref_to_doc);
tdata_t const buf = _TIFFmalloc(buf_size); // tdata_t is void*
if (!buf)
throw std::runtime_error("Cannot read TIFF file: failed allocating buffer" + ref_to_doc);
Datafield data(std::vector<const Scale*>{newEquiDivision("u (bin)", w, 0.0, double(w)),
newEquiDivision("v (bin)", h, 0.0, double(h))});
std::vector<int8_t> line_buf;
line_buf.resize(buf_size, 0);
for (uint32_t row = 0; row < h; row++) {
if (TIFFReadScanline(tiffstream, buf, row) < 0)
throw std::runtime_error("Cannot read TIFF file: error in scanline." + ref_to_doc);
memcpy(line_buf.data(), buf, buf_size);
for (unsigned col = 0; col < w; ++col) {
void* incoming = &line_buf[col * bytesPerSample];
double sample = 0;
switch (sampleFormat) {
case 1: // unsigned int
switch (bitsPerSample) {
case 8:
sample = *reinterpret_cast<uint8_t*>(incoming);
break;
case 16:
sample = *reinterpret_cast<uint16_t*>(incoming);
break;
case 32:
sample = *reinterpret_cast<uint32_t*>(incoming);
break;
default:
throw std::runtime_error("Corrupted TIFF file");
}
break;
case 2: // signed int
switch (bitsPerSample) {
case 8:
sample = *reinterpret_cast<int8_t*>(incoming);
break;
case 16:
sample = *reinterpret_cast<int16_t*>(incoming);
break;
case 32:
sample = *reinterpret_cast<int32_t*>(incoming);
break;
default:
throw std::runtime_error("Corrupted TIFF file");
}
break;
case 3: // IEEE float
sample = double(*reinterpret_cast<float*>(incoming));
break;
default:
throw std::runtime_error("Cannot read TIFF file: unexpected sample format"
+ ref_to_doc);
}
data[(h - 1 - row) * w + col] = sample;
}
}
_TIFFfree(buf);
TIFFClose(tiffstream);
return data;
}
void Util::RW::writeTiff(const Datafield& data, std::ostream& output_stream)
{
if (data.rank() != 2)
throw std::runtime_error("Cannot write TIFF file: unsupported data rank");
TIFF* tiffstream = TIFFStreamOpen("MemTIFF", &output_stream);
ASSERT(tiffstream);
const size_t m_width = data.axis(0).size();
const size_t m_height = data.axis(1).size(); // this does not exist for 1d data
//... Write header.
TIFFSetField(tiffstream, TIFFTAG_ARTIST, "BornAgain.IOFactory");
TIFFSetField(tiffstream, TIFFTAG_DATETIME, Base::System::getCurrentDateAndTime().c_str());
TIFFSetField(tiffstream, TIFFTAG_IMAGEDESCRIPTION,
"Image converted from BornAgain intensity file.");
TIFFSetField(tiffstream, TIFFTAG_SOFTWARE, "BornAgain");
const auto width = static_cast<uint32_t>(m_width);
const auto height = static_cast<uint32_t>(m_height);
TIFFSetField(tiffstream, TIFFTAG_IMAGEWIDTH, width);
TIFFSetField(tiffstream, TIFFTAG_IMAGELENGTH, height);
// output format, hardcoded here
const uint16_t bitPerSample = 32;
const uint16_t samplesPerPixel = 1;
TIFFSetField(tiffstream, TIFFTAG_BITSPERSAMPLE, bitPerSample);
TIFFSetField(tiffstream, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel);
TIFFSetField(tiffstream, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISWHITE);
//... Write data.
using sample_t = int;
const tmsize_t buf_size = sizeof(sample_t) * m_width;
const tdata_t buf = _TIFFmalloc(buf_size);
if (!buf)
throw std::runtime_error("Cannot write TIFF file: failed allocating buffer");
std::vector<sample_t> line_buf;
line_buf.resize(m_width, 0);
for (unsigned row = 0; row < (uint32_t)m_height; row++) {
for (unsigned col = 0; col < line_buf.size(); ++col)
line_buf[col] = static_cast<sample_t>(data[(m_height - 1 - row) * m_width + col]);
memcpy(buf, line_buf.data(), buf_size);
if (TIFFWriteScanline(tiffstream, buf, row) < 0)
throw std::runtime_error("Cannot write TIFF file: error in TIFFWriteScanline");
}
_TIFFfree(buf);
TIFFFlush(tiffstream);
TIFFClose(tiffstream);
}
#endif // BA_TIFF_SUPPORT
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