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/*
Copyright 2008 Brain Research Institute, Melbourne, Australia
Written by J-Donald Tournier, 27/06/08.
This file is part of MRtrix.
MRtrix 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.
MRtrix 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 MRtrix. If not, see <http://www.gnu.org/licenses/>.
08-09-2008 J-Donald Tournier <d.tournier@brain.org.au>
* fix handling of mosaic slice ordering (using SliceNormalVector entry in CSA header)
10-06-2009 J-Donald Tournier <d.tournier@brain.org.au>
* fix handling of acquisition matrix when the rows & columns are interchanged.
17-09-2009 J-Donald Tournier <d.tournier@brain.org.au>
* added preliminary support to read Philips DW information
09-12-2009 J-Donald Tournier <d.tournier@brain.org.au>
* preliminary GE gradient information support
03-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* improved GE gradient information support
16-07-2010 J-Donald Tournier <d.tournier@brain.org.au>
* check for readable data in GE private DW tags before assigning
*/
#include <glibmm/miscutils.h>
#include "file/dicom/image.h"
#include "file/dicom/series.h"
#include "file/dicom/study.h"
#include "file/dicom/patient.h"
#include "file/dicom/csa_entry.h"
namespace MR {
namespace File {
namespace Dicom {
void Image::parse_item (Element& item, bool print_DICOM_fields, bool print_CSA_fields)
{
if (print_DICOM_fields)
print (str(item) + "\n");
// is this tag top-level or per-frame:
bool is_toplevel = (item.level() == 0);
for (guint n = 0; n < item.level(); ++n) {
if (item.sequence[n].group == 0x5200U && (
item.sequence[n].element == 0x9230U || // per-frame tag
item.sequence[n].element == 0x9229U)) { // shared across frames tag
is_toplevel = true;
break;
}
}
// process image-specific or per-frame items here:
if (is_toplevel) {
switch (item.group) {
case 0x0018U:
switch (item.element) {
case 0x0050U: slice_thickness = item.get_float()[0]; return;
case 0x1310U: acq_dim[0] = MAX (item.get_uint()[0], item.get_uint()[1]);
acq_dim[1] = MAX (item.get_uint()[2], item.get_uint()[3]);
return;
case 0x0024U: sequence_name = item.get_string()[0];
if (!sequence_name.size()) return;
{
int c = sequence_name.size()-1;
while (c >= 0 && isdigit (sequence_name[c])) c--;
c++;
sequence = to<guint> (sequence_name.substr (c));
}
return;
case 0x9087U: bvalue = item.get_float()[0]; return;
case 0x9089U: G[0] = item.get_float()[0];
G[1] = item.get_float()[1];
G[2] = item.get_float()[2];
return;
}
return;
case 0x0020U:
switch (item.element) {
case 0x0011U: series_num = item.get_uint()[0]; return;
case 0x0012U: acq = item.get_uint()[0]; return;
case 0x0013U: instance = item.get_uint()[0]; return;
case 0x0032U: position_vector[0] = item.get_float()[0];
position_vector[1] = item.get_float()[1];
position_vector[2] = item.get_float()[2];
return;
case 0x0037U: orientation_x[0] = item.get_float()[0];
orientation_x[1] = item.get_float()[1];
orientation_x[2] = item.get_float()[2];
orientation_y[0] = item.get_float()[3];
orientation_y[1] = item.get_float()[4];
orientation_y[2] = item.get_float()[5];
Math::normalise (orientation_x);
Math::normalise (orientation_y);
return;
case 0x9157U: index = item.get_uint();
if (frame_dim.size() < index.size())
frame_dim.resize (index.size());
for (guint n = 0; n < index.size(); ++n)
if (frame_dim[n] < index[n])
frame_dim[n] = index[n];
return;
}
return;
case 0x0028U:
switch (item.element) {
case 0x0010U: dim[1] = item.get_uint()[0]; return;
case 0x0011U: dim[0] = item.get_uint()[0]; return;
case 0x0030U: pixel_size[0] = item.get_float()[0];
pixel_size[1] = item.get_float()[1];
return;
case 0x0100U: bits_alloc = item.get_uint()[0]; return;
case 0x1052U: scale_intercept = item.get_float()[0]; return;
case 0x1053U: scale_slope = item.get_float()[0]; return;
}
return;
case 0xFFFEU:
switch (item.element) {
case 0xE000U:
if (item.sequence.back().group == 0x5200U &&
item.sequence.back().element == 0x9230U) { // multi-frame item
if (in_frames) {
calc_distance();
frames.push_back (RefPtr<Frame> (new Frame (*this)));
frame_offset += dim[0] * dim[1] * (bits_alloc/8);
}
else
in_frames = true;
}
return;
}
return;
case 0x7FE0U:
if (item.element == 0x0010U) {
data = item.offset (item.data);
data_size = item.size;
is_BE = item.is_big_endian();
return;
}
return;
}
}
// process more non-specific stuff here:
switch (item.group) {
case 0x0008U:
if (item.element == 0x0070U) manufacturer = item.get_string()[0];
return;
case 0x0019U:
switch (item.element) { // GE DW encoding info:
case 0x10BBU: if (item.get_float().size()) G[0] = item.get_float()[0]; return;
case 0x10BCU: if (item.get_float().size()) G[1] = item.get_float()[0]; return;
case 0x10BDU: if (item.get_float().size()) G[2] = item.get_float()[0]; return;
//Siemens private DW encoding tags:
case 0x100CU: if (item.get_int().size()) bvalue = item.get_int()[0]; return;
case 0x100EU: if (item.get_float().size() == 3) {
G[0] = item.get_float()[0];
G[1] = item.get_float()[1];
G[2] = item.get_float()[2];
}
return;
}
return;
case 0x0029U: // Siemens CSA entry
if (item.element == 0x1010U || item.element == 0x1020U) {
decode_csa (item.data, item.data + item.size, print_CSA_fields);
return;
}
else return;
case 0x0043U: // GEMS_PARMS_01 block
if (item.element == 0x1039U) {
if (item.get_int().size()) bvalue = item.get_int()[0];
DW_scheme_wrt_image = true;
}
return;
case 0x2001U: // Philips DW encoding info:
if (item.element == 0x1003) bvalue = item.get_float()[0];
return;
case 0x2005U: // Philips DW encoding info:
switch (item.element) {
case 0x10B0U: G[0] = item.get_float()[0]; return;
case 0x10B1U: G[1] = item.get_float()[0]; return;
case 0x10B2U: G[2] = item.get_float()[0]; return;
}
return;
}
}
void Image::read (bool print_DICOM_fields, bool print_CSA_fields)
{
Element item;
item.set (filename);
while (item.read())
parse_item (item, print_DICOM_fields, print_CSA_fields);
calc_distance();
if (frame_offset > 0)
frames.push_back (RefPtr<Frame> (new Frame (*this)));
else if (images_in_mosaic > 0) {
if (dim[0] % acq_dim[0] || dim[1] % acq_dim[1]) {
error ("WARNING: acquisition matrix [ " + str (acq_dim[0]) + " " + str (acq_dim[1])
+ " ] does not fit into DICOM mosaic [ " + str (dim[0]) + " " + str (dim[1])
+ " ] in image \"" + filename + "\" - adjusting matrix size to suit");
acq_dim[0] = dim[0] / guint (float(dim[0]) / float(acq_dim[0]));
acq_dim[1] = dim[1] / guint (float(dim[1]) / float(acq_dim[1]));
}
gfloat xinc = pixel_size[0] * (dim[0] - acq_dim[0]) / 2.0;
gfloat yinc = pixel_size[1] * (dim[1] - acq_dim[1]) / 2.0;
for (guint i = 0; i < 3; i++)
position_vector[i] += xinc * orientation_x[i] + yinc * orientation_y[i];
row_stride = dim[0];
dim[0] = acq_dim[0];
dim[1] = acq_dim[1];
guint row_size = dim[0] * (bits_alloc/8);
guint nframes_per_row = row_stride / dim[0];
guint nx = 0, ny = 0;
for (guint z = 0; z < images_in_mosaic; z++) {
Frame* frame = new Frame (*this);
frame->frame_offset = row_size * (nx + ny * nframes_per_row * dim[1]);
for (guint n = 0; n < 3; ++n)
frame->position_vector[n] = position_vector[n] + z * slice_thickness * orientation_z[n];
frame->distance = Math::dot_product (orientation_z, frame->position_vector);
frames.push_back (RefPtr<Frame> (frame));
++nx;
if (nx >= nframes_per_row) { nx = 0; ++ny; }
}
}
for (guint n = 0; n < frames.size(); ++n)
frames[n]->data = data + frames[n]->frame_offset;
}
void Image::decode_csa (const guint8* start, const guint8* end, bool print_fields)
{
CSAEntry entry (start, end);
while (entry.parse()) {
if (print_fields)
print (str(entry) + "\n");
if (strcmp ("B_value", entry.key()) == 0) bvalue = entry.get_float();
else if (strcmp ("DiffusionGradientDirection", entry.key()) == 0) entry.get_float (G);
else if (strcmp ("NumberOfImagesInMosaic", entry.key()) == 0) images_in_mosaic = entry.get_int();
else if (strcmp ("SliceNormalVector", entry.key()) == 0) entry.get_float (orientation_z);
}
if (G[0] && bvalue)
if (fabs(G[0]) > 1.0 && fabs(G[1]) > 1.0 && fabs(G[2]) > 1.0)
bvalue = G[0] = G[1] = G[2] = 0.0;
}
std::ostream& operator<< (std::ostream& stream, const Frame& item)
{
stream << ( item.instance == UINT_MAX ? 0 : item.instance ) << "#"
<< ( item.acq == UINT_MAX ? 0 : item.acq) << ":"
<< ( item.sequence == UINT_MAX ? 0 : item.sequence ) << " "
<< item.dim[0] << "x" << item.dim[1] << ", "
<< item.pixel_size[0] << "x" << item.pixel_size[1] << " x "
<< item.slice_thickness << " mm, z = " << item.distance
<< ( item.index.size() ? ", index = " + str(item.index) : String() ) << ", [ "
<< item.position_vector[0] << " " << item.position_vector[1] << " " << item.position_vector[2] << " ] [ "
<< item.orientation_x[0] << " " << item.orientation_x[1] << " " << item.orientation_x[2] << " ] [ "
<< item.orientation_y[0] << " " << item.orientation_y[1] << " " << item.orientation_y[2] << " ]";
if (gsl_finite (item.bvalue)) {
stream << ", b = " << item.bvalue;
if (item.bvalue > 0.0)
stream << ", G = [ " << item.G[0] << " " << item.G[1] << " " << item.G[2] << " ]";
}
return stream;
}
std::ostream& operator<< (std::ostream& stream, const Image& item)
{
stream << ( item.filename.size() ? item.filename : "file not set" ) << ":\n"
<< ( item.sequence_name.size() ? item.sequence_name : "sequence not set" ) << " ["
<< (item.manufacturer.size() ? item.manufacturer : String("unknown manufacturer")) << "] "
<< (item.frames.size() > 0 ? str(item.frames.size()) + " frames with dim " + str(item.frame_dim) : String());
if (item.frames.size()) {
for (guint n = 0; n < item.frames.size(); ++n)
stream << " " << static_cast<Frame>(*item.frames[n]) << "\n";
}
else
stream << " " << static_cast<Frame>(item) << "\n";
return stream;
}
namespace {
inline void update_count (guint num, std::vector<guint>& dim, std::vector<guint>& index)
{
for (guint n = 0; n < num; ++n) {
if (dim[n] && index[n] != dim[n])
throw Exception ("dimensions mismatch in DICOM series");
index[n] = 1;
}
++index[num];
dim[num] = index[num];
}
}
std::vector<guint> Frame::count (const std::vector<Frame*>& frames)
{
std::vector<guint> dim (3, 0);
std::vector<guint> index (3, 1);
const Frame* previous = frames[0];
for (std::vector<Frame*>::const_iterator frame_it = frames.begin()+1; frame_it != frames.end(); ++frame_it) {
const Frame& frame (**frame_it);
if (frame.series_num != previous->series_num ||
frame.acq != previous->acq)
update_count (2, dim, index);
else if (frame.distance != previous->distance)
update_count (1, dim, index);
else
update_count (0, dim, index);
previous = &frame;
}
if (!dim[0]) dim[0] = 1;
if (!dim[1]) dim[1] = 1;
if (!dim[2]) dim[2] = 1;
return dim;
}
gfloat Frame::get_slice_separation (const std::vector<Frame*>& frames, guint nslices)
{
bool slicesep_warning_issued = false;
bool slicegap_warning_issued = false;
float slice_separation = frames[0]->slice_thickness;
for (guint n = 0; n < nslices-1; ++n) {
float current_slice_separation = frames[n+1]->distance - frames[n]->distance;
if (!gsl_finite (slice_separation)) {
slice_separation = current_slice_separation;
continue;
}
if (!slicegap_warning_issued) {
if (fabs (current_slice_separation - frames[n]->slice_thickness) > 1e-4) {
error ("WARNING: slice gap detected");
slicegap_warning_issued = true;
slice_separation = current_slice_separation;
}
}
if (!slicesep_warning_issued) {
if (fabs (current_slice_separation - slice_separation) > 1e-4) {
slicesep_warning_issued = true;
error ("WARNING: slice separation is not constant");
}
}
}
return slice_separation;
}
Math::Matrix Frame::get_DW_scheme (const std::vector<Frame*>& frames, guint nslices, const Math::Matrix& image_transform)
{
Math::Matrix G;
if (gsl_isnan (frames[0]->bvalue)) {
debug ("no DW encoding information found in DICOM frames");
return G;
}
const guint nDW = frames.size() / nslices;
G.allocate (nDW, 4);
const bool rotate_DW_scheme = frames[0]->DW_scheme_wrt_image;
for (guint n = 0; n < nDW; ++n) {
const Frame& frame (*frames[n*nslices]);
G(n,3) = frame.bvalue;
G(n,0) = G(n,1) = G(n,2) = 0.0;
if (G(n,3)) {
float norm = Math::magnitude (frame.G);
G(n,3) *= norm*norm;
if (norm) {
float d[] = { frame.G[0]/norm, frame.G[1]/norm, frame.G[2]/norm };
if (rotate_DW_scheme) {
G(n,0) = image_transform(0,0)*d[0] + image_transform(0,1)*d[1] - image_transform(0,2)*d[2];
G(n,1) = image_transform(1,0)*d[0] + image_transform(1,1)*d[1] - image_transform(1,2)*d[2];
G(n,2) = image_transform(2,0)*d[0] + image_transform(2,1)*d[1] - image_transform(2,2)*d[2];
}
else {
G(n,0) = -d[0];
G(n,1) = -d[1];
G(n,2) = d[2];
}
}
}
}
return G;
}
}
}
}
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