void Mosaic::execute ()
{
const std::vector<File::Entry>& files (H.get_files());
if (files.empty()) throw Exception ("no files specified in header for image \"" + H.name() + "\"");
assert (H.datatype().bits() > 1);
segsize = H.dim (0) * H.dim (1) * H.dim (2);
assert (segsize * files.size() == DataSet::voxel_count (H));
size_t bytes_per_segment = H.datatype().bytes() * segsize;
if (files.size() * bytes_per_segment > std::numeric_limits<size_t>::max())
throw Exception ("image \"" + H.name() + "\" is larger than maximum accessible memory");
debug ("loading mosaic image \"" + H.name() + "\"...");
addresses.resize (1);
addresses[0] = new uint8_t [files.size() * bytes_per_segment];
if (!addresses[0]) throw Exception ("failed to allocate memory for image \"" + H.name() + "\"");
ProgressBar progress ("reformatting DICOM mosaic images...", slices*files.size());
uint8_t* data = addresses[0];
for (size_t n = 0; n < files.size(); n++) {
File::MMap file (files[n], false, m_xdim * m_ydim * H.datatype().bytes());
size_t nx = 0, ny = 0;
for (size_t z = 0; z < slices; z++) {
size_t ox = nx*xdim;
size_t oy = ny*ydim;
for (size_t y = 0; y < ydim; y++) {
memcpy (data, file.address() + H.datatype().bytes() * (ox + m_xdim* (y+oy)), xdim * H.datatype().bytes());
data += xdim * H.datatype().bytes();
}
nx++;
if (nx >= m_xdim / xdim) {
nx = 0;
ny++;
}
++progress;
}
}
segsize = std::numeric_limits<size_t>::max();
}
void Default::copy_to_mem (const Header& header)
{
DEBUG ("loading image \"" + header.name() + "\"...");
addresses.resize (files.size() > 1 && header.datatype().bits() *segsize != 8*size_t (bytes_per_segment) ? files.size() : 1);
addresses[0].reset (new uint8_t [files.size() * bytes_per_segment]);
if (!addresses[0])
throw Exception ("failed to allocate memory for image \"" + header.name() + "\"");
if (is_new) memset (addresses[0].get(), 0, files.size() * bytes_per_segment);
else {
for (size_t n = 0; n < files.size(); n++) {
File::MMap file (files[n], false, false, bytes_per_segment);
memcpy (addresses[0].get() + n*bytes_per_segment, file.address(), bytes_per_segment);
}
}
if (addresses.size() > 1)
for (size_t n = 1; n < addresses.size(); n++)
addresses[n].reset (addresses[0].get() + n*bytes_per_segment);
else segsize = std::numeric_limits<size_t>::max();
}
void Mosaic::load ()
{
if (files.empty())
throw Exception ("no files specified in header for image \"" + name + "\"");
assert (datatype.bits() > 1);
size_t bytes_per_segment = datatype.bytes() * segsize;
if (files.size() * bytes_per_segment > std::numeric_limits<size_t>::max())
throw Exception ("image \"" + name + "\" is larger than maximum accessible memory");
DEBUG ("loading mosaic image \"" + name + "\"...");
addresses.resize (1);
addresses[0].reset (new uint8_t [files.size() * bytes_per_segment]);
if (!addresses[0])
throw Exception ("failed to allocate memory for image \"" + name + "\"");
ProgressBar progress ("reformatting DICOM mosaic images...", slices*files.size());
uint8_t* data = addresses[0].get();
for (size_t n = 0; n < files.size(); n++) {
File::MMap file (files[n], false, false, m_xdim * m_ydim * datatype.bytes());
size_t nx = 0, ny = 0;
for (size_t z = 0; z < slices; z++) {
size_t ox = nx*xdim;
size_t oy = ny*ydim;
for (size_t y = 0; y < ydim; y++) {
memcpy (data, file.address() + datatype.bytes() * (ox + m_xdim* (y+oy)), xdim * datatype.bytes());
data += xdim * datatype.bytes();
}
nx++;
if (nx >= m_xdim / xdim) {
nx = 0;
ny++;
}
++progress;
}
}
segsize = std::numeric_limits<size_t>::max();
}
void dicom_to_mapper (
MR::Image::Mapper& dmap,
MR::Image::Header& H,
std::vector< RefPtr<Series> >& series_list)
{
assert (series_list.size() > 0);
H.format = FormatDICOM;
Patient* patient (series_list[0]->study->patient);
String sbuf = ( patient->name.size() ? patient->name : "unnamed" );
sbuf += " " + format_ID (patient->ID);
if (series_list[0]->modality.size()) sbuf += String (" [") + series_list[0]->modality + "]";
if (series_list[0]->name.size()) sbuf += String (" ") + series_list[0]->name;
H.comments.push_back (sbuf);
H.name = sbuf;
// build up sorted list of frames:
std::vector<Frame*> frames;
// loop over series list:
for (std::vector< RefPtr<Series> >::const_iterator series_it = series_list.begin(); series_it != series_list.end(); ++series_it) {
Series& series (**series_it);
try {
series.read();
}
catch (Exception) {
throw Exception ("error reading series " + str (series.number) + " of DICOM image \"" + H.name + "\"");
}
std::sort (series.begin(), series.end());
// loop over images in each series:
for (Series::const_iterator image_it = series.begin(); image_it != series.end(); ++image_it) {
Image& image (**image_it);
// if multi-frame, loop over frames in image:
if (image.frames.size()) {
std::sort (image.frames.begin(), image.frames.end());
for (std::vector< RefPtr<Frame> >::const_iterator frame_it = image.frames.begin(); frame_it != image.frames.end(); ++frame_it)
frames.push_back (&**frame_it);
}
// otherwise add image frame:
else
frames.push_back (&image);
}
}
std::vector<guint> dim = Frame::count (frames);
if (dim[0] > 1) { // switch axes so slice dim is inner-most:
std::vector<Frame*> list (frames);
std::vector<Frame*>::iterator it = frames.begin();
for (guint k = 0; k < dim[2]; ++k)
for (guint i = 0; i < dim[0]; ++i)
for (guint j = 0; j < dim[1]; ++j)
*(it++) = list[i+dim[0]*(j+dim[1]*k)];
}
gfloat slice_separation = Frame::get_slice_separation (frames, dim[1]);
if (series_list[0]->study->name.size()) {
sbuf = "study: " + series_list[0]->study->name;
H.comments.push_back (sbuf);
}
if (patient->DOB.size()) {
sbuf = "DOB: " + format_date (patient->DOB);
H.comments.push_back (sbuf);
}
if (series_list[0]->date.size()) {
sbuf = "DOS: " + format_date (series_list[0]->date);
if (series_list[0]->time.size())
sbuf += " " + format_time (series_list[0]->time);
H.comments.push_back (sbuf);
}
MR::Image::Axes& axes (H.axes);
const Image& image (*(*series_list[0])[0]);
guint nchannels = image.frames.size() ? 1 : image.data_size / (image.dim[0] * image.dim[1] * (image.bits_alloc/8));
if (nchannels > 1)
info ("data segment is larger than expected from image dimensions - interpreting as multi-channel data");
axes.set_ndim (3 + (dim[0]*dim[2]>1) + (nchannels>1));
guint current_axis = 3;
guint current_stride = 0;
add_axis ("channel", axes, current_axis, current_stride, nchannels);
axes.axis[0] = current_stride++;
axes.dim[0] = image.dim[0];
axes.vox[0] = image.pixel_size[0];
axes.desc[0] = MR::Image::Axis::left_to_right;
axes.units[0] = MR::Image::Axis::millimeters;
axes.axis[1] = current_stride++;
axes.dim[1] = image.dim[1];
axes.vox[1] = image.pixel_size[1];
axes.desc[1] = MR::Image::Axis::posterior_to_anterior;
axes.units[1] = MR::Image::Axis::millimeters;
axes.axis[2] = current_stride++;
axes.dim[2] = dim[1];
axes.vox[2] = slice_separation;
axes.desc[2] = MR::Image::Axis::inferior_to_superior;
axes.units[2] = MR::Image::Axis::millimeters;
add_axis ("volume", axes, current_axis, current_stride, dim[0]*dim[2]);
if (image.bits_alloc == 8) H.data_type = DataType::UInt8;
else if (image.bits_alloc == 16) {
H.data_type = DataType::UInt16;
if (image.is_BE) H.data_type.set_flag (DataType::BigEndian);
else H.data_type.set_flag (DataType::LittleEndian);
}
else throw Exception ("unexpected number of allocated bits per pixel (" + str (image.bits_alloc)
+ ") in file \"" + H.name + "\"");
H.offset = image.scale_intercept;
H.scale = image.scale_slope;
Math::Matrix M(4,4);
M(0,0) = -image.orientation_x[0];
M(1,0) = -image.orientation_x[1];
M(2,0) = image.orientation_x[2];
M(3,0) = 0.0;
M(0,1) = -image.orientation_y[0];
M(1,1) = -image.orientation_y[1];
M(2,1) = image.orientation_y[2];
M(3,1) = 0.0;
M(0,2) = -image.orientation_z[0];
M(1,2) = -image.orientation_z[1];
M(2,2) = image.orientation_z[2];
M(3,2) = 0.0;
M(0,3) = -image.position_vector[0];
M(1,3) = -image.position_vector[1];
M(2,3) = image.position_vector[2];
M(3,3) = 1.0;
H.set_transform (M);
H.DW_scheme = Frame::get_DW_scheme (frames, dim[1], M);
for (guint n = 1; n < frames.size(); ++n) // check consistency of data scaling:
if (frames[n]->scale_intercept != frames[n-1]->scale_intercept ||
frames[n]->scale_slope != frames[n-1]->scale_slope)
throw Exception ("unable to load series due to inconsistent data scaling between DICOM images");
if (image.frames.size()) { // need to preload and re-arrange:
ProgressBar::init (frames.size(), "DICOM image contains multiple frames - reformating...");
guint8* mem = NULL;
try {
mem = new guint8 [H.memory_footprint()];
if (!mem) throw;
}
catch (...) {
throw Exception ("failed to allocate memory for image data!");
}
guint8* dest = mem;
const guint row_stride = nchannels * frames[0]->row_stride * (frames[0]->bits_alloc/8);
const guint row_size = nchannels * frames[0]->dim[0] * (frames[0]->bits_alloc/8);
File::MMap mmap;
for (guint n = 0; n < frames.size(); ++n) {
mmap.init (frames[n]->filename);
mmap.map();
const guint8* src = (guint8*) mmap.address() + frames[n]->data;
for (guint row = 0; row < frames[n]->dim[1]; ++row) {
memcpy (dest, src, row_size);
dest += row_size;
src += row_stride;
}
ProgressBar::inc();
}
ProgressBar::done();
dmap.add (mem);
}
else { // use standard backend:
for (guint n = 0; n < frames.size(); ++n) {
const Image* image = static_cast<const Image*> (frames[n]);
dmap.add (image->filename, image->data);
}
}
}
