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/* Copyright (c) 2008-2022 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#ifndef __file_dicom_image_h__
#define __file_dicom_image_h__
#include <memory>
#include "datatype.h"
#include "types.h"
#include "file/dicom/element.h"
namespace MR {
namespace File {
namespace Dicom {
class Series;
class Element;
class Frame { MEMALIGN(Frame)
public:
Frame () {
acq_dim[0] = acq_dim[1] = dim[0] = dim[1] = instance =
series_num = acq = sequence = echo_index = grad_number = UINT_MAX;
samples_per_pixel = 1;
position_vector[0] = position_vector[1] = position_vector[2] = NaN;
orientation_x[0] = orientation_x[1] = orientation_x[2] = NaN;
orientation_y[0] = orientation_y[1] = orientation_y[2] = NaN;
orientation_z[0] = orientation_z[1] = orientation_z[2] = NaN;
distance = NaN;
pixel_size[0] = pixel_size[1] = slice_thickness = slice_spacing = NaN;
scale_intercept = 0.0;
scale_slope = 1.0;
bvalue = G[0] = G[1] = G[2] = G_prs[0] = G_prs[1] = G_prs[2] = NaN;
data = bits_alloc = data_size = frame_offset = 0;
transfer_syntax_supported = true;
ignore_series_num = false;
pe_axis = 3;
pe_sign = 0;
philips_orientation = '\0';
pixel_bandwidth = bandwidth_per_pixel_phase_encode = echo_time = inversion_time = repetition_time = flip_angle = partial_fourier = time_after_start = NaN;
echo_train_length = 0;
bipolar_flag = readoutmode_flag = 0;
}
size_t acq_dim[2], dim[2], series_num, instance, acq, sequence, echo_index, grad_number, samples_per_pixel;
Eigen::Vector3d position_vector, orientation_x, orientation_y, orientation_z, G, G_prs;
default_type distance, pixel_size[2], slice_thickness, slice_spacing, scale_slope, scale_intercept, bvalue;
size_t data, bits_alloc, data_size, frame_offset;
std::string filename, image_type;
bool DW_scheme_wrt_image, transfer_syntax_supported, ignore_series_num;
size_t pe_axis;
int pe_sign;
char philips_orientation;
Time acquisition_time;
default_type pixel_bandwidth, bandwidth_per_pixel_phase_encode, echo_time, inversion_time, repetition_time, flip_angle, partial_fourier, time_after_start;
size_t echo_train_length;
size_t bipolar_flag, readoutmode_flag;
vector<uint32_t> index;
vector<default_type> flip_angles;
bool operator< (const Frame& frame) const {
if (!ignore_series_num && series_num != frame.series_num)
return series_num < frame.series_num;
if (image_type != frame.image_type)
return image_type < frame.image_type;
if (acq != frame.acq)
return acq < frame.acq;
if (std::isfinite (distance) && std::isfinite (frame.distance) && distance != frame.distance)
return distance < frame.distance;
for (size_t n = index.size(); n--;)
if (index[n] != frame.index[n])
return index[n] < frame.index[n];
if (echo_index != frame.echo_index)
return echo_index < frame.echo_index;
if (std::isfinite (echo_time) && echo_time != frame.echo_time)
return echo_time < frame.echo_time;
if (grad_number != frame.grad_number)
return grad_number < frame.grad_number;
if (sequence != frame.sequence)
return sequence < frame.sequence;
if (instance != frame.instance)
return instance < frame.instance;
return false;
}
void calc_distance ()
{
if (!std::isfinite (orientation_z[0]))
orientation_z = orientation_x.cross (orientation_y);
else {
if (!orientation_x.allFinite() || !orientation_y.allFinite())
throw Exception ("slice orientation information missing from DICOM header!");
Eigen::Vector3d normal = orientation_x.cross (orientation_y);
if (normal.dot (orientation_z) < 0.0)
orientation_z = -normal;
else
orientation_z = normal;
}
if (!position_vector.allFinite())
throw Exception ("slice position information missing from DICOM header!");
orientation_z.normalize();
distance = orientation_z.dot (position_vector);
}
bool is_philips_iso () const {
if (philips_orientation == '\0')
return false;
return (philips_orientation == 'I' && bvalue > 0.0);
}
static vector<size_t> count (const vector<Frame*>& frames);
static default_type get_slice_separation (const vector<Frame*>& frames, size_t nslices);
static std::string get_DW_scheme (const vector<Frame*>& frames, const size_t nslices, const transform_type& image_transform);
static Eigen::MatrixXd get_PE_scheme (const vector<Frame*>& frames, const size_t nslices);
friend std::ostream& operator<< (std::ostream& stream, const Frame& item);
};
class Image : public Frame { MEMALIGN(Image)
public:
Image (Series* parent = nullptr) :
series (parent),
images_in_mosaic (0),
is_BE (false),
in_frames (false) { }
Series* series;
size_t images_in_mosaic;
std::string sequence_name, manufacturer;
bool is_BE, in_frames;
vector<float> mosaic_slices_timing;
vector<uint32_t> frame_dim;
vector<std::shared_ptr<Frame>> frames;
void read ();
void parse_item (Element& item, const std::string& dirname = "");
void decode_csa (const uint8_t* start, const uint8_t* end);
KeyValues read_csa_ascii (const vector<std::string>& data);
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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