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/* -*- mia-c++ -*-
*
* This file is part of MIA - a toolbox for medical image analysis
* Copyright (c) Leipzig, Madrid 1999-2014 Gert Wollny
*
* MIA is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MIA; if not, see <http://www.gnu.org/licenses/>.
*
*/
#include <string>
#include <mia/core.hh>
#include <mia/3d.hh>
NS_MIA_USE;
using namespace std;
using namespace boost;
inline bool am_big_endian()
{
#ifdef WORDS_BIGENDIAN
return true;
#else
return false;
#endif
}
const SProgramDescription g_description = {
{pdi_group, "Image conversion"},
{pdi_short, "Convert raw data into a 3D image"},
{pdi_description,"This program is used to convert raw data into 3D images "
"with apropriate metadata."},
{pdi_example_descr, "pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr"},
{pdi_example_code, "-i data.raw -o image.hdr -s \"<10,20,30>\" -k \"<1.2,2.3,3.4>\" -r ushort"}
};
template <typename I>
void handle_endian(I b, I e)
{
typedef typename iterator_traits<I>::value_type Pixel;
typedef union {
char s[sizeof(Pixel)];
Pixel v;
} shuffle;
switch (sizeof(Pixel)) {
case 2:
while (b != e) {
shuffle s;
s.v = *b;
swap(s.s[0], s.s[1]);
*b = s.v;
++b;
}
break;
case 4:
while (b != e) {
shuffle s;
s.v = *b;
swap(s.s[0], s.s[3]);
swap(s.s[1], s.s[2]);
*b = s.v;
++b;
}
break;
case 8:
while (b != e) {
shuffle s;
s.v = *b;
swap(s.s[0],s.s[7]);
swap(s.s[1],s.s[6]);
swap(s.s[2],s.s[5]);
swap(s.s[3],s.s[4]);
*b = s.v;
++b;
}
break;
default: // just to silence the warning
return;
}
}
template <typename Image>
std::shared_ptr<C3DImage > read_image_type(CInputFile& in_file, const C3DBounds& size, const C3DFVector& scale, bool big_endian)
{
typedef typename Image::value_type T;
Image *image = new Image(size);
std::shared_ptr<C3DImage > result(image);
if (!image) {
stringstream errmsg;
errmsg << "Unable to allocate image of size " << size;
throw runtime_error(errmsg.str());
}
if (fread(&(*image)(0,0,0), sizeof(T), image->size(), in_file) != image->size()) {
throw runtime_error("Not enough data for specified image size in input file.");
}
image->set_voxel_size(scale);
if ( (sizeof(T) > 1 ) && (big_endian != am_big_endian())) {
handle_endian(image->begin(), image->end());
}
return result;
}
std::shared_ptr<C3DImage > read_image(CInputFile& in_file, int pixel_type, const C3DBounds& size, const C3DFVector& scale, bool high_endian)
{
switch (pixel_type) {
case it_ubyte: return read_image_type<C3DUBImage>(in_file, size, scale, high_endian);
case it_sbyte: return read_image_type<C3DSBImage>(in_file, size, scale, high_endian);
case it_sshort:return read_image_type<C3DSSImage>(in_file, size, scale, high_endian);
case it_ushort:return read_image_type<C3DUSImage>(in_file, size, scale, high_endian);
case it_sint: return read_image_type<C3DSIImage>(in_file, size, scale, high_endian);
case it_uint: return read_image_type<C3DUIImage>(in_file, size, scale, high_endian);
case it_float: return read_image_type<C3DFImage> (in_file, size, scale, high_endian);
case it_double: return read_image_type<C3DDImage> (in_file, size, scale, high_endian);
default:
throw invalid_argument("given input pixel format not supported");
};
}
int do_main(int argc, char *argv[])
{
EPixelType pixel_type = it_ubyte;
bool high_endian = false;
C3DBounds size(0,0,0);
C3DFVector scale(1,1,1);
string in_filename;
string out_filename;
size_t skip = 0;
const C3DImageIOPluginHandler::Instance& imageio = C3DImageIOPluginHandler::instance();
if (imageio.get_set().empty())
throw runtime_error("Sorry, no 3D output formats supported");
CCmdOptionList options(g_description);
options.add(make_opt( in_filename, "in-file", 'i', "input file name", CCmdOptionFlags::required_input));
options.add(make_opt( out_filename, "out-file", 'o', "output file name", CCmdOptionFlags::required_output, &imageio));
options.add(make_opt( pixel_type, CPixelTypeDict, "repn", 'r',"input pixel type "));
options.add(make_opt( high_endian, "big-endian", 'b', "input data is big endian"));
options.add(make_opt( scale, "scale", 'f', "scale of input voxels <FX,FY,FZ>"));
options.add(make_opt( skip, "skip", 'k', "skip number of bytes from beginning of file"));
options.add(make_opt( size, "size", 's', "size of input <NX,NY,NZ>", CCmdOptionFlags::required));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
return EXIT_SUCCESS;
CInputFile in_file(in_filename);
if ( !in_file )
throw runtime_error(string("Unable to open ")+ in_filename);
C3DBounds bsize(size);
C3DFVector fscale(scale);
C3DImageVector out_images;
if (fseek(in_file, skip, SEEK_SET) == 0)
out_images.push_back(read_image(in_file, pixel_type, bsize, fscale, high_endian));
else
throw create_exception<invalid_argument>("Skipping ", skip, " bytes of file '",
in_filename, "' failed:", strerror(errno));
return !imageio.save(out_filename, out_images);
}
#include <mia/internal/main.hh>
MIA_MAIN(do_main);
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