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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_mgh_h__
#define __file_mgh_h__
#include <sstream>
#include "header.h"
#include "raw.h"
#include "file/gz.h"
#include "file/nifti_utils.h"
#define MGH_HEADER_SIZE 90
#define MGH_DATA_OFFSET 284
#define MGH_TYPE_UCHAR 0
#define MGH_TYPE_SHORT 4
#define MGH_TYPE_INT 1
#define MGH_TYPE_FLOAT 3
#define MGH_TAG_OLD_COLORTABLE 1
#define MGH_TAG_OLD_USEREALRAS 2
#define MGH_TAG_CMDLINE 3
#define MGH_TAG_USEREALRAS 4
#define MGH_TAG_COLORTABLE 5
#define MGH_TAG_GCAMORPH_GEOM 10
#define MGH_TAG_GCAMORPH_TYPE 11
#define MGH_TAG_GCAMORPH_LABELS 12
#define MGH_TAG_OLD_SURF_GEOM 20
#define MGH_TAG_SURF_GEOM 21
#define MGH_TAG_OLD_MGH_XFORM 30
#define MGH_TAG_MGH_XFORM 31
#define MGH_TAG_GROUP_AVG_SURFACE_AREA 32
#define MGH_TAG_AUTO_ALIGN 33
#define MGH_TAG_SCALAR_DOUBLE 40
#define MGH_TAG_PEDIR 41
#define MGH_TAG_MRI_FRAME 42
#define MGH_TAG_FIELDSTRENGTH 43
#define MGH_STRLEN 1024
#define MGH_MATRIX_STRLEN (4*4*100)
#define MGH_FRAME_TYPE_ORIGINAL 0
#define MGH_FRAME_TYPE_DIFFUSION_AUGMENTED 1
namespace MR
{
class Header;
namespace File
{
namespace MGH
{
int32_t string_to_tag_ID (const std::string& key);
std::string tag_ID_to_string (const int32_t tag);
template <typename ValueType, class Input>
inline ValueType fetch (Input& in)
{
ValueType value;
in.read (reinterpret_cast<char*> (&value), sizeof (ValueType));
if (in.eof())
throw int(1);
value = ByteOrder::BE (value);
return value;
}
template <typename ValueType, class Output>
inline void store (ValueType value, Output& out)
{
value = ByteOrder::BE (value);
out.write (reinterpret_cast<char*> (&value), sizeof (ValueType));
}
inline bool check (Header& H, size_t num_axes)
{
if (num_axes < 3) throw Exception ("cannot create MGH image with less than 3 dimensions");
if (num_axes > 4) throw Exception ("cannot create MGH image with more than 4 dimensions");
H.ndim() = num_axes;
if (H.datatype().is_complex())
throw Exception ("MGH file format does not support complex types");
switch (H.datatype()() & (DataType::Type | DataType::Signed)) {
case DataType::Bit:
case DataType::UInt8:
H.datatype() = DataType::UInt8; break;
case DataType::Int8:
case DataType::UInt16:
case DataType::Int16:
H.datatype() = DataType::Int16BE; break;
case DataType::UInt32:
case DataType::Int32:
case DataType::UInt64:
case DataType::Int64:
H.datatype() = DataType::Int32BE; break;
case DataType::Float32:
case DataType::Float64:
H.datatype() = DataType::Float32BE; break;
default: throw Exception ("Unsupported data type for MGH format (" + std::string(H.datatype().specifier()) + ")");
}
return true;
}
typedef struct
{
int32_t type; // code for what is stored in this frame
float32 TE; // echo time
float32 TR; // recovery time
float32 flip; // flip angle
float32 TI; // time-to-inversion
float32 TD; // delay time
// Note that in the import / export code, TM is loaded with a float32 here, even though
// TM actually appears in the augmented diffusion section
int32_t sequence_type; // see SEQUENCE* constants
float32 echo_spacing;
float32 echo_train_len; // length of the echo train
float32 read_dir[3]; // read-out direction in RAS coords
float32 pe_dir[3]; // phase-encode direction in RAS coords
float32 slice_dir[3]; // slice direction in RAS coords
int32_t label; // index into CLUT
char name[MGH_STRLEN]; // human-readable description of frame contents
int32_t dof; // for stat maps (e.g. # of subjects)
Eigen::Matrix<default_type, 4, 4>* m_ras2vox;
float32 thresh;
int32_t units; // e.g. UNITS_PPM, UNITS_RAD_PER_SEC, ...
// for Herr Dr. Prof. Dr. Dr. Witzel
// directions: maybe best in both reference frames
// or just 3 coordinates and a switch which frame it is?
float64 DX, DY, DZ, DR, DP, DS;
// B-value
float64 bvalue;
// Mixing time
float64 TM;
// What kind of diffusion scan is this (can be an enum)
// stejskal-tanner,trse,steam etc....
int64_t diffusion_type;
// Gradient values
int64_t D1_ramp, D1_flat; float64 D1_amp;
int64_t D2_ramp, D2_flat; float64 D2_amp;
int64_t D3_ramp, D3_flat; float64 D3_amp;
int64_t D4_ramp, D4_flat; float64 D4_amp;
} mri_frame ;
template <class Input>
void read_header (Header& H, Input& in)
{
auto version = fetch<int32_t> (in);
if (version != 1)
throw Exception ("image \"" + H.name() + "\" is not in MGH format (version != 1)");
auto width = fetch<int32_t> (in);
auto height = fetch<int32_t> (in);
auto depth = fetch<int32_t> (in);
auto nframes = fetch<int32_t> (in);
auto type = fetch<int32_t> (in);
fetch<int32_t> (in); // dof - ignored
auto RAS = fetch<int16_t> (in);
const size_t ndim = (nframes > 1) ? 4 : 3;
H.ndim() = ndim;
H.size (0) = width;
H.size (1) = height;
H.size (2) = depth;
if (ndim == 4)
H.size (3) = nframes;
H.spacing (0) = fetch<float32> (in);
H.spacing (1) = fetch<float32> (in);
H.spacing (2) = fetch<float32> (in);
for (size_t i = 0; i != ndim; ++i)
H.stride (i) = i + 1;
DataType dtype;
switch (type) {
case MGH_TYPE_UCHAR: dtype = DataType::UInt8; break;
case MGH_TYPE_SHORT: dtype = DataType::Int16BE; break;
case MGH_TYPE_INT: dtype = DataType::Int32BE; break;
case MGH_TYPE_FLOAT: dtype = DataType::Float32BE; break;
default: throw Exception ("unknown data type for MGH image \"" + H.name() + "\" (" + str (type) + ")");
}
H.datatype() = dtype;
H.reset_intensity_scaling();
transform_type& M (H.transform());
if (RAS) {
M(0,0) = fetch<float32> (in);
M(1,0) = fetch<float32> (in);
M(2,0) = fetch<float32> (in);
M(0,1) = fetch<float32> (in);
M(1,1) = fetch<float32> (in);
M(2,1) = fetch<float32> (in);
M(0,2) = fetch<float32> (in);
M(1,2) = fetch<float32> (in);
M(2,2) = fetch<float32> (in);
M(0,3) = fetch<float32> (in);
M(1,3) = fetch<float32> (in);
M(2,3) = fetch<float32> (in);
for (size_t i = 0; i < 3; ++i) {
for (size_t j = 0; j < 3; ++j)
M(i,3) -= 0.5 * H.size(j) * H.spacing(j) * M(i,j);
}
} else {
// Default transformation matrix, assumes coronal orientation
M(0,0) = -1.0; M(0,1) = 0.0; M(0,2) = 0.0; M(0,3) = 0.0;
M(1,0) = 0.0; M(1,1) = 0.0; M(1,2) = -1.0; M(1,3) = 0.0;
M(2,0) = 0.0; M(2,1) = +1.0; M(2,2) = 0.0; M(2,3) = 0.0;
}
}
template <class Input>
void read_other (Header& H, Input& in)
{
// First, encapsulate some functionalities for cleanliness...
// TODO These may well be shared with the FreeSurfer surface file formats
auto read_matrix = [] (Input& in)
{
char buffer[MGH_MATRIX_STRLEN];
in.read (buffer, MGH_MATRIX_STRLEN);
// There's also a string before the 16 floating-point values, the FreeSurfer code
// discards it immediately
char ch[100];
Eigen::Matrix<default_type, 4, 4> M;
sscanf (buffer, "%s %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf",
ch,
&M(0,0), &M(0,1), &M(0,2), &M(0,3),
&M(1,0), &M(1,1), &M(1,2), &M(1,3),
&M(2,0), &M(2,1), &M(2,2), &M(2,3),
&M(3,0), &M(3,1), &M(3,2), &M(3,3));
return M;
};
auto read_mri_frame = [&] (Input& in, const int64_t len)
{
const int64_t fstart = in.tellg();
const size_t nframes = H.ndim() == 4 ? H.size(3) : 1;
std::string table;
Eigen::IOFormat format (Eigen::StreamPrecision, Eigen::DontAlignCols, " ", " ", "", "", "", "");
for (size_t frame_index = 0; frame_index != nframes; ++frame_index) {
mri_frame frame;
frame.type = fetch<int32_t> (in);
frame.TE = fetch<float32> (in);
frame.TR = fetch<float32> (in);
frame.flip = fetch<float32> (in);
frame.TI = fetch<float32> (in);
frame.TD = fetch<float32> (in);
// FreeSurfer loads TM with a float32 here, even though TM is in the diffusion section and is a float64...
fetch<float32> (in);
frame.TM = 0.0;
frame.sequence_type = fetch<int32_t> (in);
frame.echo_spacing = fetch<float32> (in);
frame.echo_train_len = fetch<float32> (in);
for (size_t i = 0; i != 3; i++)
frame.read_dir[i] = fetch<float32> (in);
for (size_t i = 0; i != 3; i++)
frame.pe_dir[i] = fetch<float32> (in);
for (size_t i = 0; i != 3; i++)
frame.slice_dir[i] = fetch<float32> (in);
frame.label = fetch<int32_t> (in);
in.read (frame.name, MGH_STRLEN);
frame.dof = fetch<int32_t> (in);
// Single matrix is read here; use the same function as that for importing MGH_TAG_AUTO_ALIGN
fetch<int32_t> (in); // Skip the tag ID absorbed by znzTAGreadStart()
fetch<int64_t> (in); // Also skip the length
frame.m_ras2vox = new Eigen::Matrix<default_type, 4, 4> (read_matrix (in));
frame.thresh = fetch<float32> (in);
frame.units = fetch<int32_t> (in);
std::string line = str(frame.type) + "," + str(frame.TE) + "," + str(frame.TR) + "," + str(frame.flip) + ","
+ str(frame.TI) + "," + str(frame.TD) + ","
+ str(frame.sequence_type) + "," + str(frame.echo_spacing) + "," + str(frame.echo_train_len) + ","
+ str(frame.read_dir[0]) + "," + str(frame.read_dir[1]) + "," + str(frame.read_dir[2]) + ","
+ str(frame.pe_dir[0]) + "," + str(frame.pe_dir[1]) + "," + str(frame.pe_dir[2]) + ","
+ str(frame.slice_dir[0]) + "," + str(frame.slice_dir[1]) + "," + str(frame.slice_dir[2]) + ","
+ str(frame.label) + "," + frame.name + "," + str(frame.dof) + ","
+ str(frame.m_ras2vox->format (format)) + ","
+ str(frame.thresh) + "," + str(frame.units);
delete frame.m_ras2vox; frame.m_ras2vox = nullptr;
if (frame.type == MGH_FRAME_TYPE_DIFFUSION_AUGMENTED) {
frame.DX = fetch<float64> (in);
frame.DY = fetch<float64> (in);
frame.DZ = fetch<float64> (in);
frame.DR = fetch<float64> (in);
frame.DP = fetch<float64> (in);
frame.DS = fetch<float64> (in);
frame.bvalue = fetch<float64> (in);
frame.TM = fetch<float64> (in);
frame.D1_ramp = fetch<int64_t> (in);
frame.D1_flat = fetch<int64_t> (in);
frame.D1_amp = fetch<float64> (in);
frame.D2_ramp = fetch<int64_t> (in);
frame.D2_flat = fetch<int64_t> (in);
frame.D2_amp = fetch<float64> (in);
frame.D3_ramp = fetch<int64_t> (in);
frame.D3_flat = fetch<int64_t> (in);
frame.D3_amp = fetch<float64> (in);
frame.D4_ramp = fetch<int64_t> (in);
frame.D4_flat = fetch<int64_t> (in);
frame.D4_amp = fetch<float64> (in);
line += "," + str(frame.DX) + "," + str(frame.DY) + "," + str(frame.DZ) + ","
+ str(frame.DR) + "," + str(frame.DP) + "," + str(frame.DS) + ","
+ str(frame.bvalue) + "," + str(frame.TM) + ","
+ str(frame.D1_ramp) + "," + str(frame.D1_flat) + "," + str(frame.D1_amp) + ","
+ str(frame.D2_ramp) + "," + str(frame.D2_flat) + "," + str(frame.D2_amp) + ","
+ str(frame.D3_ramp) + "," + str(frame.D3_flat) + "," + str(frame.D3_amp) + ","
+ str(frame.D4_ramp) + "," + str(frame.D4_flat) + "," + str(frame.D4_amp);
}
add_line (table, line);
}
// Test to see if the correct amount of data has been read
// (the expected length of the field is reported as part of the tag)
const int64_t fend = in.tellg();
const int64_t empty_space_len = len - (fend - fstart);
if (empty_space_len > 0) {
char buffer[empty_space_len];
in.read (buffer, empty_space_len);
}
return table;
};
auto read_colourtable_V1 = [&] (Input& in, const int32_t nentries)
{
if (!nentries)
throw Exception ("Error reading colour table from file \"" + H.name() + "\": No entries");
std::string table;
const int32_t filename_length = fetch<int32_t> (in);
std::string filename (filename_length, '\0');
in.read (const_cast<char*> (filename.data()), filename_length);
for (int32_t structure = 0; structure != nentries; ++structure) {
const int32_t structurename_length = fetch<int32_t> (in);
if (structurename_length < 0)
throw Exception ("Error reading colour table from file \"" + H.name() + "\": Negative structure name length");
std::string structurename (structurename_length, '\0');
in.read (const_cast<char*> (structurename.data()), structurename_length);
while (structurename.size() && !structurename.back())
structurename.pop_back();
const int32_t r = fetch<int32_t> (in);
const int32_t g = fetch<int32_t> (in);
const int32_t b = fetch<int32_t> (in);
const int32_t t = fetch<int32_t> (in);
const int32_t a = 255 - t; // Alpha = 255 - transparency
add_line (table, structurename + "," + str(r) + "," + str(g) + "," + str(b) + "," + str(a));
}
return table;
};
auto read_colourtable_V2 = [&] (Input& in)
{
const int32_t nentries = fetch<int32_t> (in);
if (!nentries)
throw Exception ("Error reading colour table from file \"" + H.name() + "\": No entries");
vector<std::string> table;
const int32_t filename_length = fetch<int32_t> (in);
std::string filename (filename_length, '\0');
in.read (const_cast<char*> (filename.data()), filename_length);
const int32_t num_entries_to_read = fetch<int32_t> (in);
for (int32_t i = 0; i != num_entries_to_read; ++i) {
const int32_t structure = fetch<int32_t> (in);
if (structure < 0)
throw Exception ("Error reading colour table from file \"" + H.name() + "\": Negative structure index (" + str(structure) + ")");
if (size_t (structure) < table.size() && table[structure].size())
throw Exception ("Error reading colour table from file \"" + H.name() + "\": Duplicate structure index (" + str(structure) + ")");
else if (size_t (structure) >= table.size())
table.resize (structure + 1, std::string());
const int32_t structurename_length = fetch<int32_t> (in);
if (structurename_length < 0)
throw Exception ("Error reading colour table from file \"" + H.name() + "\": Negative structure name length");
std::string structurename (structurename_length, '\0');
in.read (const_cast<char*> (structurename.data()), structurename_length);
while (structurename.size() && !structurename.back())
structurename.pop_back();
const int32_t r = fetch<int32_t> (in);
const int32_t g = fetch<int32_t> (in);
const int32_t b = fetch<int32_t> (in);
const int32_t t = fetch<int32_t> (in);
const int32_t a = 255 - t; // Alpha = 255 - transparency
table[structure] = structurename + "," + str(r) + "," + str(g) + "," + str(b) + "," + str(a);
}
std::string result;
for (size_t index = 0; index != table.size(); ++index) {
if (table[index].size())
add_line (result, str(index) + "," + table[index]);
}
return result;
};
// Start the function read_other() proper
try {
// fetch() will throw an int(1) straight away if these data don't exist
H.keyval()["MGH_TR"] = str(fetch<float32> (in), 6);
H.keyval()["MGH_flip"] = str(fetch<float32> (in) * 180.0 / Math::pi, 6); // Radians in MGHO -> degrees in header
H.keyval()["MGH_TE"] = str(fetch<float32> (in), 6);
H.keyval()["MGH_TI"] = str(fetch<float32> (in), 6);
fetch<float32> (in); // fov - ignored
do {
auto id = fetch<int32_t> (in);
int64_t size;
if (id == MGH_TAG_OLD_MGH_XFORM)
size = fetch<int32_t> (in) - 1;
else if (id == MGH_TAG_OLD_SURF_GEOM
|| id == MGH_TAG_OLD_USEREALRAS
|| id == MGH_TAG_OLD_COLORTABLE)
size = 0;
else if (id <= 0)
throw Exception ("Invalid tag (" + str(id) + ") in MGH format \"other data\"");
else
size = fetch<int64_t> (in);
std::string content (size+1, '\0');
switch (id) {
case MGH_TAG_MRI_FRAME:
H.keyval()[tag_ID_to_string(id)] = read_mri_frame (in, size);
break;
case MGH_TAG_OLD_COLORTABLE:
{
const int32_t version = fetch<int32_t> (in);
if (version > 0) {
const int32_t nentries = version;
H.keyval()[tag_ID_to_string(id)] = read_colourtable_V1 (in, nentries);
} else if (version == -2) {
H.keyval()[tag_ID_to_string(id)] = read_colourtable_V2 (in);
} else {
throw Exception ("Error reading colour table from file \"" + H.name() + "\": Unknown version (" + str(version) + ")");
}
}
break;
case MGH_TAG_OLD_MGH_XFORM:
case MGH_TAG_MGH_XFORM:
in.read (const_cast<char*> (content.data()), size);
H.keyval()[tag_ID_to_string(id)] = content;
// Don't care whether or not we can actually access this file...
break;
case MGH_TAG_CMDLINE:
in.read (const_cast<char*> (content.data()), size);
// Should only appear one line at a time
add_line (H.keyval()["command_history"], content);
break;
case MGH_TAG_AUTO_ALIGN:
{
// Imports data into a 4x4 matrix, and stores in header by converting to string
Eigen::IOFormat format (10, Eigen::DontAlignCols, ",", "\n", "", "", "", "");
std::stringstream sstream;
sstream << read_matrix (in).format (format);
H.keyval()[tag_ID_to_string(id)] = sstream.str();
}
break;
case MGH_TAG_PEDIR:
in.read (const_cast<char*> (content.data()), size);
H.keyval()[tag_ID_to_string(id)] = content;
break;
case MGH_TAG_FIELDSTRENGTH: {
// This field is written with TAGwrite() rather than znzwriteFloat()
// Therefore, the byte order is NOT forced to big-endian
// As a consequence, this import will only work if the system that
// created the file, and the one reading the file, have the
// same endianness
float32 field_strength = fetch<float32>(in);
#ifndef MRTRIX_IS_BIG_ENDIAN
ByteOrder::swap (field_strength);
#endif
H.keyval()[tag_ID_to_string(id)] = str(field_strength);
}
break;
default: // FreeSurfer doesn't actually perform any import of any other fields
in.read (const_cast<char*> (content.data()), size);
break;
}
} while (!in.eof());
} catch (int) { }
}
template <class Output>
void write_header (const Header& H, Output& out)
{
const size_t ndim = H.ndim();
if (ndim > 4)
throw Exception ("MGH file format does not support images of more than 4 dimensions");
vector<size_t> axes;
auto M = File::NIfTI::adjust_transform (H, axes);
store<int32_t> (1, out); // version
store<int32_t> (H.size (axes[0]), out); // width
store<int32_t> ((ndim > 1) ? H.size (axes[1]) : 1, out); // height
store<int32_t> ((ndim > 2) ? H.size (axes[2]) : 1, out); // depth
store<int32_t> ((ndim > 3) ? H.size (3) : 1, out); // nframes
int32_t type;
switch (H.datatype()()) {
case DataType::UInt8: type = MGH_TYPE_UCHAR; break;
case DataType::Int16BE: type = MGH_TYPE_SHORT; break;
case DataType::Int32BE: type = MGH_TYPE_INT; break;
case DataType::Float32BE: type = MGH_TYPE_FLOAT; break;
default: throw Exception ("Error in MGH file format header write: invalid datatype (" + std::string(H.datatype().specifier()) + ")");
}
store<int32_t> (type, out); // type
store<int32_t> (0, out); // dof
store<int16_t> (1, out); // goodRASFlag
store<float32> (H.spacing (axes[0]), out); // spacing_x
store<float32> (H.spacing (axes[1]), out); // spacing_y
store<float32> (H.spacing (axes[2]), out); // spacing_z
float32 c[3] = { 0.0f, 0.0f, 0.0f };
for (size_t i = 0; i != 3; ++i) {
default_type offset = M(i, 3);
for (size_t j = 0; j != 3; ++j)
offset += 0.5 * H.size(axes[j]) * H.spacing(axes[j]) * M(i,j);
switch (i) {
case 0: c[0] = offset; break;
case 1: c[1] = offset; break;
case 2: c[2] = offset; break;
}
}
store<float32> (M(0,0), out); // x_r
store<float32> (M(1,0), out); // x_a
store<float32> (M(2,0), out); // x_s
store<float32> (M(0,1), out); // y_r
store<float32> (M(1,1), out); // y_a
store<float32> (M(2,1), out); // y_s
store<float32> (M(0,2), out); // z_r
store<float32> (M(1,2), out); // z_a
store<float32> (M(2,2), out); // z_s
store<float32> (c[0], out); // c_r
store<float32> (c[1], out); // c_a
store<float32> (c[2], out); // c_s
}
template <class Output>
void write_other (const Header& H, Output& out)
{
class Tag
{
public:
Tag() : id (0), content() { }
Tag (const int32_t i, const std::string& s) : id (i), content (s) { }
void set (const int32_t i, const std::string& s) { id = i; content = s; }
int32_t id;
std::string content;
};
// Function znzWriteMatrix() is used for both MGH_TAG_AUTO_ALIGN tag entries,
// and in znzTAGwriteMRIframes() for the VOX2RAS matrix.
auto write_matrix = [] (const Eigen::Matrix<default_type, 4, 4>& M, Output& out)
{
char buffer[MGH_MATRIX_STRLEN];
memset (buffer, 0x00, MGH_MATRIX_STRLEN);
sprintf (buffer, "AutoAlign %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf %10lf",
M(0,0), M(0,1), M(0,2), M(0,3),
M(1,0), M(1,1), M(1,2), M(1,3),
M(2,0), M(2,1), M(2,2), M(2,3),
M(3,0), M(3,1), M(3,2), M(3,3));
store<int32_t> (MGH_TAG_AUTO_ALIGN, out);
store<int64_t> (MGH_MATRIX_STRLEN, out);
out.write (buffer, MGH_MATRIX_STRLEN);
};
auto write_mri_frames = [&] (const std::string& table, Output& out)
{
const size_t nframes = H.ndim() == 4 ? H.size(3) : 1;
const auto lines = split_lines (table);
if (lines.size() != nframes) {
WARN ("Error writing MRI frame data to output image (image has " + str(nframes) + " volumes, frame data tables has " + str(lines.size()) + " rows); omitting information from output image");
return;
}
vector<mri_frame> frames (nframes);
for (size_t frame_index = 0; frame_index != nframes; ++frame_index) {
const auto entries = split (lines[frame_index], ",", false);
if (entries.size() != 24 && entries.size() != 45) {
WARN ("Error writing MRI frame data to output image (frame data table has line with " + str(entries.size()) + " entries, expected 24 or 45); omitting information from output image");
return;
}
mri_frame& frame (frames[frame_index]);
frame.type = to<int32_t> (entries[0]);
frame.TE = to<float32> (entries[1]);
frame.TR = to<float32> (entries[2]);
frame.flip = to<float32> (entries[3]);
frame.TI = to<float32> (entries[4]);
frame.TD = to<float32> (entries[5]);
// When stored in an MRtrix3 header key:value entry, TM is NOT included in the list at this point
frame.sequence_type = to<int32_t> (entries[6]);
frame.echo_spacing = to<float32> (entries[7]);
frame.echo_train_len = to<float32> (entries[8]);
for (size_t i = 0; i != 3; ++i)
frame.read_dir[i] = to<float32> (entries[9+i]);
for (size_t i = 0; i != 3; ++i)
frame.pe_dir[i] = to<float32> (entries[12+i]);
for (size_t i = 0; i != 3; ++i)
frame.slice_dir[i] = to<float32> (entries[15+i]);
frame.label = to<int32_t> (entries[18]);
strcpy (frame.name, entries[19].c_str());
frame.dof = to<int32_t> (entries[20]);
frame.m_ras2vox = new Eigen::Matrix<default_type, 4, 4> (Eigen::Matrix<default_type, 4, 4>::Zero());
const auto M = split (entries[21], " ");
if (M.size() != 16) {
WARN ("Error writing MRI frame data to output image (expected RAS2vox matrix with 16 entries, read " + str(M.size()) + "); omitting information from output image");
return;
}
(*frame.m_ras2vox)(0,0) = to<default_type> (M[0]);
(*frame.m_ras2vox)(0,1) = to<default_type> (M[1]);
(*frame.m_ras2vox)(0,2) = to<default_type> (M[2]);
(*frame.m_ras2vox)(0,3) = to<default_type> (M[3]);
(*frame.m_ras2vox)(1,0) = to<default_type> (M[4]);
(*frame.m_ras2vox)(1,1) = to<default_type> (M[5]);
(*frame.m_ras2vox)(1,2) = to<default_type> (M[6]);
(*frame.m_ras2vox)(1,3) = to<default_type> (M[7]);
(*frame.m_ras2vox)(2,0) = to<default_type> (M[8]);
(*frame.m_ras2vox)(2,1) = to<default_type> (M[9]);
(*frame.m_ras2vox)(2,2) = to<default_type> (M[10]);
(*frame.m_ras2vox)(2,3) = to<default_type> (M[11]);
(*frame.m_ras2vox)(3,0) = to<default_type> (M[12]);
(*frame.m_ras2vox)(3,1) = to<default_type> (M[13]);
(*frame.m_ras2vox)(3,2) = to<default_type> (M[14]);
(*frame.m_ras2vox)(3,3) = to<default_type> (M[15]);
frame.thresh = to<float32> (entries[22]);
frame.units = to<int32_t> (entries[23]);
if (frame.type == MGH_FRAME_TYPE_DIFFUSION_AUGMENTED) {
if (entries.size() != 45) {
WARN ("Error writing MRI frame data to output image (frame indicated as diffusion-augmented, but does not have sufficient data); omitting information from output image");
return;
}
frame.DX = to<float64> (entries[25]);
frame.DY = to<float64> (entries[26]);
frame.DZ = to<float64> (entries[27]);
frame.DR = to<float64> (entries[28]);
frame.DP = to<float64> (entries[29]);
frame.DS = to<float64> (entries[30]);
frame.bvalue = to<float64> (entries[31]);
frame.TM = to<float64> (entries[32]);
frame.diffusion_type = to<int64_t> (entries[33]);
frame.D1_ramp = to<int64_t> (entries[34]);
frame.D1_flat = to<int64_t> (entries[35]);
frame.D1_amp = to<float64> (entries[36]);
frame.D2_ramp = to<int64_t> (entries[37]);
frame.D2_flat = to<int64_t> (entries[38]);
frame.D2_amp = to<float64> (entries[39]);
frame.D3_ramp = to<int64_t> (entries[40]);
frame.D3_flat = to<int64_t> (entries[41]);
frame.D3_amp = to<float64> (entries[42]);
frame.D4_ramp = to<int64_t> (entries[43]);
frame.D4_flat = to<int64_t> (entries[44]);
frame.D4_amp = to<float64> (entries[45]);
}
}
// That's right: The size allocated is based on the size of a class, which
// contains a pointer to a matrix; hence probably why they had to add
// a safety factor...
// TODO See if this can be reduced
const int64_t len = 10 * nframes * sizeof(mri_frame);
store<int32_t> (MGH_TAG_MRI_FRAME, out);
store<int64_t> (len, out);
const int64_t fstart = out.tellp();
for (auto frame : frames) {
store<int32_t> (frame.type, out);
store<float32> (frame.TE, out);
store<float32> (frame.TR, out);
store<float32> (frame.flip, out);
store<float32> (frame.TI, out);
store<float32> (frame.TD, out);
// Once again, have to account for the fact that FreeSurfer reads / writes a single-precision
// floating-point value for TM here, even though TM is a double and resides in the
// augmented diffusion section
store<float32> (0.0f, out);
store<int32_t> (frame.sequence_type, out);
store<float32> (frame.echo_spacing, out);
store<float32> (frame.echo_train_len, out);
for (size_t i = 0; i != 3; ++i)
store<float32> (frame.read_dir[i], out);
for (size_t i = 0; i != 3; ++i)
store<float32> (frame.pe_dir[i], out);
for (size_t i = 0; i != 3; ++i)
store<float32> (frame.slice_dir[i], out);
store<int32_t> (frame.label, out);
out.write (frame.name, MGH_STRLEN);
store<int32_t> (frame.dof, out);
write_matrix (*frame.m_ras2vox, out); delete frame.m_ras2vox; frame.m_ras2vox = nullptr;
store<float32> (frame.thresh, out);
store<int32_t> (frame.units, out);
if (frame.type == MGH_FRAME_TYPE_DIFFUSION_AUGMENTED) {
store<float64> (frame.DX, out);
store<float64> (frame.DY, out);
store<float64> (frame.DZ, out);
store<float64> (frame.DR, out);
store<float64> (frame.DP, out);
store<float64> (frame.DS, out);
store<float64> (frame.bvalue, out);
store<float64> (frame.TM, out);
store<int64_t> (frame.diffusion_type, out);
store<int64_t> (frame.D1_ramp, out);
store<int64_t> (frame.D1_flat, out);
store<float64> (frame.D1_amp, out);
store<int64_t> (frame.D2_ramp, out);
store<int64_t> (frame.D2_flat, out);
store<float64> (frame.D2_amp, out);
store<int64_t> (frame.D3_ramp, out);
store<int64_t> (frame.D3_flat, out);
store<float64> (frame.D3_amp, out);
store<int64_t> (frame.D4_ramp, out);
store<int64_t> (frame.D4_flat, out);
store<float64> (frame.D4_amp, out);
}
}
const int64_t fend = out.tellp();
const int64_t extra_space_len = len - (fend - fstart);
if (extra_space_len > 0) {
char buffer[extra_space_len];
memset (buffer, 0x00, extra_space_len);
out.write (buffer, extra_space_len);
}
};
auto write_colourtable_V1 = [] (const std::string& table, Output& out)
{
const auto lines = split_lines (table);
if (!lines.size())
return;
store<int32_t> (MGH_TAG_OLD_COLORTABLE, out);
store<int32_t> (lines.size(), out);
const std::string filename = "INTERNAL";
store<int32_t> (filename.size()+1, out);
out.write (filename.c_str(), filename.size()+1);
for (const auto& line : lines) {
const auto entries = split (line, ",", true);
if (entries.size() != 5)
throw Exception ("Error writing colour table to file: Line has " + str(entries.size()) + " fields, expected 5");
// Name,Red,Green,Blue,Transparency
store<int32_t> (entries[0].size()+1, out);
out.write (entries[0].c_str(), entries[0].size()+1);
store<int32_t> (to<int32_t> (entries[1]), out);
store<int32_t> (to<int32_t> (entries[2]), out);
store<int32_t> (to<int32_t> (entries[3]), out);
store<int32_t> (255 - to<int32_t> (entries[4]), out);
}
};
auto write_colourtable_V2 = [] (const std::string& table, Output& out)
{
store<int32_t> (MGH_TAG_OLD_COLORTABLE, out);
store<int32_t> (-2, out);
// Need to find out the maximum node index
const auto lines = split_lines (table);
int32_t max_index = 0;
for (auto line : lines) {
const auto entries = split (line, ",", true);
if (entries.size() != 6)
throw Exception ("Error writing colour table to file: Line has " + str(entries.size()) + " fields, expected 6");
const int32_t index = to<int32_t> (entries[0]);
max_index = std::max (max_index, index);
}
store<int32_t> (max_index+1, out);
const std::string filename = "INTERNAL";
store<int32_t> (filename.size()+1, out);
out.write (filename.c_str(), filename.size()+1);
// Actual number of entries in the table
store<int32_t> (lines.size(), out);
for (const auto& line : lines) {
const auto entries = split (line, ",", true);
// Index,Name,Red,Green,Blue,Transparency
store<int32_t> (to<int32_t> (entries[0]), out);
store<int32_t> (entries[1].size()+1, out);
out.write (entries[1].c_str(), entries[1].size()+1);
store<int32_t> (to<int32_t> (entries[2]), out);
store<int32_t> (to<int32_t> (entries[3]), out);
store<int32_t> (to<int32_t> (entries[4]), out);
store<int32_t> (255 - to<int32_t> (entries[5]), out);
}
};
float32 tr = 0.0f; /*!< milliseconds */
float32 flip_angle = 0.0f; /*!< radians */
float32 te = 0.0f; /*!< milliseconds */
float32 ti = 0.0f; /*!< milliseconds */
float32 fov = 0.0f; /*!< IGNORE THIS FIELD (data is inconsistent) */
Tag transform_tag;
vector<Tag> tags; /*!< variable length char strings */
std::unique_ptr<Eigen::Matrix<default_type, 4, 4>> auto_align_matrix;
std::string pe_dir ("UNKNOWN");
float32 field_strength = NaN;
std::string mri_frames, colour_table;
vector<Tag> cmdline_tags;
for (auto entry : H.keyval()) {
if (entry.first == "command_history") {
for (auto line : split_lines (entry.second))
cmdline_tags.push_back (Tag (MGH_TAG_CMDLINE, line));
} else if (entry.first.size() < 5 || entry.first.substr(0, 4) != "MGH_") {
continue;
}
if (entry.first == "MGH_TR") {
tr = to<float32> (entry.second);
} else if (entry.first == "MGH_flip") {
flip_angle = to<float32> (entry.second) * Math::pi / 180.0;
} else if (entry.first == "MGH_TE") {
te = to<float32> (entry.second);
} else if (entry.first == "MGH_TI") {
ti = to<float32> (entry.second);
} else {
const auto id = string_to_tag_ID (entry.first);
if (id == MGH_TAG_MRI_FRAME) {
mri_frames = entry.second;
} else if (id == MGH_TAG_MGH_XFORM) {
transform_tag.set (MGH_TAG_MGH_XFORM, entry.second);
} else if (id == MGH_TAG_AUTO_ALIGN) {
auto_align_matrix.reset (new Eigen::Matrix<default_type, 4, 4> (Eigen::Matrix<default_type, 4, 4>::Zero()));
const auto lines = split_lines (entry.second);
if (lines.size() != 4)
throw Exception ("Error parsing auto align header entry for MGH format: Invalid number of lines (" + str(lines.size()) + "; should be 4)");
for (size_t row = 0; row != 4; ++row) {
const auto entries = split (strip(lines[row]), ", ", true);
if (entries.size() != 4)
throw Exception ("Error parsing auto align header entry for MGH format: Invalid number of entries on line " + str(row) + " (" + str(entries.size()) + "; should be 4)");
for (size_t col = 0; col != 4; ++col)
(*auto_align_matrix) (row, col) = to<default_type> (entries[col]);
}
} else if (id == MGH_TAG_PEDIR) {
pe_dir = entry.second;
} else if (id == MGH_TAG_FIELDSTRENGTH) {
field_strength = to<float32> (entry.second);
} else if (id == MGH_TAG_COLORTABLE || id == MGH_TAG_OLD_COLORTABLE) {
colour_table = entry.second;
} else if (id) {
tags.push_back (Tag (id, entry.second));
}
}
}
// Although we could theoretically avoid writing any metadata here at all if there were no interesting
// data to write, the fact that "command_history" will always have at least one entry (corresponding
// to the currently-executing command) means that MGH_TAG_CMDLINE will always have at least one entry
store<float32> (tr, out);
store<float32> (flip_angle, out);
store<float32> (te, out);
store<float32> (ti, out);
store<float32> (fov, out);
if (transform_tag.content.size()) {
store<int32_t> (transform_tag.id, out);
store<int64_t> (transform_tag.content.size(), out);
out.write (transform_tag.content.c_str(), transform_tag.content.size());
}
// FreeSurfer appears to write all other tag data in a single batch...
// Not sure how it is prepared though.
// Nevertheless, their referenced code seems to write a single size field,
// then a large batch of "tag data" all together; which is different to
// what we're doing here. What I don't understand is how, if the size
// of this "tag data" is the next thing written (and is only written if
// non-zero), a reader function can distinguish this size entry from a
// tag ID.
for (const auto& tag : tags) {
store<int32_t> (tag.id, out);
store<int64_t> (tag.content.size()+1, out);
out.write (tag.content.c_str(), tag.content.size()+1);
}
if (auto_align_matrix)
write_matrix (*auto_align_matrix, out);
store<int32_t> (MGH_TAG_PEDIR, out);
store<int64_t> (pe_dir.size()+1, out);
out.write (pe_dir.c_str(), pe_dir.size() + 1);
if (std::isfinite (field_strength)) {
store<int32_t> (MGH_TAG_FIELDSTRENGTH, out);
store<int64_t> (sizeof (float32), out);
// FreeSurfer uses znzTAGwrite() to write the field strength, which means it gets
// written with the native endianness of the system, rather than being
// forced to big-endian like the rest of the format.
out.write (reinterpret_cast<char*> (&field_strength), sizeof (float32));
}
if (mri_frames.size())
write_mri_frames (mri_frames, out);
if (colour_table.size()) {
const std::string first_line = colour_table.substr (0, colour_table.find_first_of ('\n'));
const auto entries = split (first_line, ",", true);
switch (entries.size()) {
case 5: write_colourtable_V1 (colour_table, out); break;
case 6: write_colourtable_V2 (colour_table, out); break;
default: WARN ("Malformed colour table in header (incorrect number of columns); not written to output image"); break;
}
}
for (const auto& tag : cmdline_tags) {
store<int32_t> (tag.id, out);
store<int64_t> (tag.content.size()+1, out);
out.write (tag.content.c_str(), tag.content.size()+1);
}
}
}
}
}
#endif
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