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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)
03-03-2010 J-Donald Tournier <d.tournier@brain.org.au>
* improved GE gradient information support
*/
#ifndef __file_dicom_image_h__
#define __file_dicom_image_h__
#include "ptr.h"
#include "math/vector.h"
#include "file/dicom/element.h"
namespace MR {
namespace File {
namespace Dicom {
class Series;
class Element;
class Frame {
public:
Frame () {
acq_dim[0] = acq_dim[1] = dim[0] = dim[1] = row_stride = instance = series_num = acq = sequence = UINT_MAX;
position_vector[0] = position_vector[1] = position_vector[2] = GSL_NAN;
orientation_x[0] = orientation_x[1] = orientation_x[2] = GSL_NAN;
orientation_y[0] = orientation_y[1] = orientation_y[2] = GSL_NAN;
orientation_z[0] = orientation_z[1] = orientation_z[2] = GSL_NAN;
distance = GSL_NAN;
pixel_size[0] = pixel_size[1] = slice_thickness = GSL_NAN;
scale_intercept = 0.0;
scale_slope = 1.0;
bvalue = G[0] = G[1] = G[2] = GSL_NAN;
data = bits_alloc = data_size = frame_offset = 0;
DW_scheme_wrt_image = false;
}
guint acq_dim[2], dim[2], row_stride, series_num, instance, acq, sequence;
gfloat position_vector[3], orientation_x[3], orientation_y[3], orientation_z[3], distance;
gfloat pixel_size[2], slice_thickness, scale_slope, scale_intercept;
gfloat bvalue, G[3];
guint data, bits_alloc, data_size, frame_offset;
String filename;
bool DW_scheme_wrt_image;
std::vector<guint32> index;
bool operator< (const Frame& frame) const {
if (series_num != frame.series_num) return series_num < frame.series_num;
if (acq != frame.acq) return acq < frame.acq;
assert (!gsl_isnan(distance));
assert (!gsl_isnan(frame.distance));
if (distance != frame.distance) return distance < frame.distance;
for (guint n = index.size(); n--;)
if (index[n] != frame.index[n])
return index[n] < frame.index[n];
if (sequence != frame.sequence) return sequence < frame.sequence;
if (instance != frame.instance) return instance < frame.instance;
return false;
}
void calc_distance ()
{
if (gsl_isnan (orientation_z[0]))
Math::cross_product (orientation_z, orientation_x, orientation_y);
else {
float normal[3];
Math::cross_product (normal, orientation_x, orientation_y);
if (Math::dot_product (normal, orientation_z) < 0.0) {
orientation_z[0] = -normal[0];
orientation_z[1] = -normal[1];
orientation_z[2] = -normal[2];
}
else {
orientation_z[0] = normal[0];
orientation_z[1] = normal[1];
orientation_z[2] = normal[2];
}
}
row_stride = dim[0];
Math::normalise (orientation_z);
distance = Math::dot_product (orientation_z, position_vector);
}
static std::vector<guint> count (const std::vector<Frame*>& frames);
static gfloat get_slice_separation (const std::vector<Frame*>& frames, guint nslices);
static Math::Matrix get_DW_scheme (const std::vector<Frame*>& frames, guint nslices, const Math::Matrix& image_transform);
friend std::ostream& operator<< (std::ostream& stream, const Frame& item);
};
class Image : public Frame {
public:
Image (Series* parent = NULL) :
series (parent),
images_in_mosaic (0),
is_BE (false),
in_frames (false) { }
Series* series;
guint images_in_mosaic;
String sequence_name, manufacturer;
bool is_BE, in_frames;
std::vector<guint32> frame_dim;
std::vector< RefPtr<Frame> > frames;
void read (bool print_DICOM_fields = false, bool print_CSA_fields = false);
void parse_item (Element& item, bool print_DICOM_fields = false, bool print_CSA_fields = false);
void decode_csa (const guint8* start, const guint8* end, bool print_fields = false);
bool operator< (const Image& ima) const {
return Frame::operator< (ima);
}
friend std::ostream& operator<< (std::ostream& stream, const Image& item);
};
}
}
}
#endif
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