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classdef AcquisitionHeader < handle
properties
version = uint16([]); % First unsigned int indicates the version %
flags = uint64([]); % bit field with flags %
measurement_uid = uint32([]); % Unique ID for the measurement %
scan_counter = uint32([]); % Current acquisition number in the measurement %
acquisition_time_stamp = uint32([]); % Acquisition clock %
physiology_time_stamp = uint32([]); % Physiology time stamps, e.g. ecg, breating, etc. %
number_of_samples = uint16([]); % Number of samples acquired %
available_channels = uint16([]); % Available coils %
active_channels = uint16([]); % Active coils on current acquisiton %
channel_mask = uint64([]); % Mask to indicate which channels are active. Support for 1024 channels %
discard_pre = uint16([]); % Samples to be discarded at the beginning of acquisition %
discard_post = uint16([]); % Samples to be discarded at the end of acquisition %
center_sample = uint16([]); % Sample at the center of k-space %
encoding_space_ref = uint16([]); % Reference to an encoding space, typically only one per acquisition %
trajectory_dimensions = uint16([]); % Indicates the dimensionality of the trajectory vector (0 means no trajectory) %
sample_time_us = single([]); % Time between samples in micro seconds, sampling BW %
position = single([]); % Three-dimensional spatial offsets from isocenter %
read_dir = single([]); % Directional cosines of the readout/frequency encoding %
phase_dir = single([]); % Directional cosines of the phase encoding %
slice_dir = single([]); % Directional cosines of the slice %
patient_table_position = single([]); % Patient table off-center %
idx = struct( ... % Encoding loop counters, see above %
'kspace_encode_step_1', uint16([]), ...
'kspace_encode_step_2', uint16([]), ...
'average', uint16([]), ...
'slice', uint16([]), ...
'contrast', uint16([]), ...
'phase', uint16([]), ...
'repetition', uint16([]), ...
'set', uint16([]), ...
'segment', uint16([]), ...
'user', uint16([]));
user_int = int32([]); % Free user parameters %
user_float = single([]); % Free user parameters %
end
properties(Constant)
FLAGS = struct( ...
'ACQ_FIRST_IN_ENCODE_STEP1', 1, ...
'ACQ_LAST_IN_ENCODE_STEP1', 2, ...
'ACQ_FIRST_IN_ENCODE_STEP2', 3, ...
'ACQ_LAST_IN_ENCODE_STEP2', 4, ...
'ACQ_FIRST_IN_AVERAGE', 5, ...
'ACQ_LAST_IN_AVERAGE', 6, ...
'ACQ_FIRST_IN_SLICE', 7, ...
'ACQ_LAST_IN_SLICE', 8, ...
'ACQ_FIRST_IN_CONTRAST', 9, ...
'ACQ_LAST_IN_CONTRAST', 10, ...
'ACQ_FIRST_IN_PHASE', 11, ...
'ACQ_LAST_IN_PHASE', 12, ...
'ACQ_FIRST_IN_REPETITION', 13, ...
'ACQ_LAST_IN_REPETITION', 14, ...
'ACQ_FIRST_IN_SET', 15, ...
'ACQ_LAST_IN_SET', 16, ...
'ACQ_FIRST_IN_SEGMENT', 17, ...
'ACQ_LAST_IN_SEGMENT', 18, ...
'ACQ_IS_NOISE_MEASUREMENT', 19, ...
'ACQ_IS_PARALLEL_CALIBRATION', 20, ...
'ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING', 21, ...
'ACQ_IS_REVERSE', 22, ...
'ACQ_IS_NAVIGATION_DATA', 23, ...
'ACQ_IS_PHASECORR_DATA', 24, ...
'ACQ_LAST_IN_MEASUREMENT', 25, ...
'ACQ_IS_HPFEEDBACK_DATA', 26, ...
'ACQ_IS_DUMMYSCAN_DATA', 27, ...
'ACQ_IS_RTFEEDBACK_DATA', 28, ...
'ACQ_IS_SURFACECOILCORRECTIONSCAN_DATA', 29, ...
'ACQ_USER1', 57, ...
'ACQ_USER2', 58, ...
'ACQ_USER3', 59, ...
'ACQ_USER4', 60, ...
'ACQ_USER5', 61, ...
'ACQ_USER6', 62, ...
'ACQ_USER7', 63, ...
'ACQ_USER8', 64);
end
methods
function obj = AcquisitionHeader(arg)
% Constructor
switch nargin
case 0
% No argument constructor
% initialize to a single acquisition header
extend(obj,1);
case 1
% One argument constructor
if isstruct(arg)
% plain struct
fromStruct(obj,arg);
elseif (length(arg)==1 && ismrmrd.util.isInt(arg)) == 1
% number
extend(obj,arg);
elseif isa(arg,'uint8')
% Byte array
fromBytes(obj,arg);
else
% Unknown type
error('Unknown argument type.')
end
otherwise
error('Wrong number of arguments.')
end
end
function nacq = getNumber(obj)
% Return the number of headers
nacq = length(obj.version);
end
function hdr = select(obj, range)
% Return a copy of a range of acquisition headers
% create an empty acquisition header
M = length(range);
hdr = ismrmrd.AcquisitionHeader(M);
% Fill
hdr.version = obj.version(range);
hdr.flags = obj.flags(range);
hdr.measurement_uid = obj.measurement_uid(range);
hdr.scan_counter = obj.scan_counter(range);
hdr.acquisition_time_stamp = obj.acquisition_time_stamp(range);
hdr.physiology_time_stamp = obj.physiology_time_stamp(:,range);
hdr.number_of_samples = obj.number_of_samples(range);
hdr.available_channels = obj.available_channels(range);
hdr.active_channels = obj.active_channels(range);
hdr.channel_mask = obj.channel_mask(:,range);
hdr.discard_pre = obj.discard_pre(range);
hdr.discard_post = obj.discard_post(range);
hdr.center_sample = obj.center_sample(range);
hdr.encoding_space_ref = obj.encoding_space_ref(range);
hdr.trajectory_dimensions = obj.trajectory_dimensions(range);
hdr.sample_time_us = obj.sample_time_us(range);
hdr.position = obj.position(:,range);
hdr.read_dir = obj.read_dir(:,range);
hdr.phase_dir = obj.phase_dir(:,range);
hdr.slice_dir = obj.slice_dir(:,range);
hdr.patient_table_position = obj.patient_table_position(:,range);
hdr.idx.kspace_encode_step_1 = obj.idx.kspace_encode_step_1(range);
hdr.idx.kspace_encode_step_2 = obj.idx.kspace_encode_step_2(range);
hdr.idx.average = obj.idx.average(range);
hdr.idx.slice = obj.idx.slice(range);
hdr.idx.contrast = obj.idx.contrast(range);
hdr.idx.phase = obj.idx.phase(range);
hdr.idx.repetition = obj.idx.repetition(range);
hdr.idx.set = obj.idx.set(range);
hdr.idx.segment = obj.idx.segment(range);
hdr.idx.user = obj.idx.user(:,range);
hdr.user_int = obj.user_int(:,range);
hdr.user_float = obj.user_float(:,range);
end
function extend(obj,N)
% Extend with blank header
range = obj.getNumber + (1:N);
obj.version(1,range) = zeros(1,N,'uint16');
obj.flags(1,range) = zeros(1,N,'uint64');
obj.measurement_uid(1,range) = zeros(1,N,'uint32');
obj.scan_counter(1,range) = zeros(1,N,'uint32');
obj.acquisition_time_stamp(1,range) = zeros(1,N,'uint32');
obj.physiology_time_stamp(1:3,range) = zeros(3,N,'uint32');
obj.number_of_samples(1,range) = zeros(1,N,'uint16');
obj.available_channels(1,range) = zeros(1,N,'uint16');
obj.active_channels(1,range) = zeros(1,N,'uint16');
obj.channel_mask(1:16,range) = zeros(16,N,'uint64');
obj.discard_pre(1,range) = zeros(1,N,'uint16');
obj.discard_post(1,range) = zeros(1,N,'uint16');
obj.center_sample(1,range) = zeros(1,N,'uint16');
obj.encoding_space_ref(1,range) = zeros(1,N,'uint16');
obj.trajectory_dimensions(1,range) = zeros(1,N,'uint16');
obj.sample_time_us(1,range) = zeros(1,N,'uint16');
obj.position(1:3,range) = zeros(3,N,'single');
obj.read_dir(1:3,range) = zeros(3,N,'single');
obj.phase_dir(1:3,range) = zeros(3,N,'single');
obj.slice_dir(1:3,range) = zeros(3,N,'single');
obj.patient_table_position(1:3,range) = zeros(3,N,'single');
obj.idx.kspace_encode_step_1(1,range) = zeros(1,N,'uint16');
obj.idx.kspace_encode_step_2(1,range) = zeros(1,N,'uint16');
obj.idx.average(1,range) = zeros(1,N,'uint16');
obj.idx.slice(1,range) = zeros(1,N,'uint16');
obj.idx.contrast(1,range) = zeros(1,N,'uint16');
obj.idx.phase(1,range) = zeros(1,N,'uint16');
obj.idx.repetition(1,range) = zeros(1,N,'uint16');
obj.idx.set(1,range) = zeros(1,N,'uint16');
obj.idx.segment(1,range) = zeros(1,N,'uint16');
obj.idx.user(1:8,range) = zeros(8,N,'uint16');
obj.user_int(1:8,range) = zeros(8,N,'int32');
obj.user_float(1:8,range) = zeros(8,N,'single');
end
function append(obj, head)
% Append a header
Nstart = obj.getNumber + 1;
Nend = obj.getNumber + length(head.version);
Nrange = Nstart:Nend;
obj.version(1,Nrange) = hdr.version(:);
obj.flags(1,Nrange) = hdr.flags(:);
obj.measurement_uid(1,Nrange) = hdr.measurement_uid(:);
obj.scan_counter(1,Nrange) = hdr.scan_counter(:);
obj.acquisition_time_stamp(1,Nrange) = hdr.acquisition_time_stamp(:);
obj.physiology_time_stamp(:,Nrange) = hdr.physiology_time_stamp(:);
obj.number_of_samples(1,Nrange) = hdr.number_of_samples(:);
obj.available_channels(1,Nrange) = hdr.available_channels(:);
obj.active_channels(1,Nrange) = hdr.active_channels(:);
obj.channel_mask(:,Nrange) = hdr.channel_mask(:);
obj.discard_pre(1,Nrange) = hdr.discard_pre(:);
obj.discard_post(1,Nrange) = hdr.discard_post(:);
obj.center_sample(1,Nrange) = hdr.center_sample(:);
obj.encoding_space_ref(1,Nrange) = hdr.encoding_space_ref(:);
obj.trajectory_dimensions(1,Nrange) = hdr.trajectory_dimensions(:);
obj.sample_time_us(1,Nrange) = hdr.sample_time_us(:);
obj.position(:,Nrange) = hdr.position(:);
obj.read_dir(:,Nrange) = hdr.read_dir(:);
obj.phase_dir(:,Nrange) = hdr.phase_dir(:);
obj.slice_dir(:,Nrange) = hdr.slice_dir(:);
obj.patient_table_position(:,Nrange) = hdr.patient_table_position(:);
obj.idx.kspace_encode_step_1(1,Nrange) = hdr.idx.kspace_encode_step_1(:);
obj.idx.kspace_encode_step_2(1,Nrange) = hdr.idx.kspace_encode_step_2(:);
obj.idx.average(1,Nrange) = hdr.idx.average(:);
obj.idx.slice(1,Nrange) = hdr.idx.slice(:);
obj.idx.contrast(1,Nrange) = hdr.idx.contrast(:);
obj.idx.phase(1,Nrange) = hdr.idx.phase(:);
obj.idx.repetition(1,Nrange) = hdr.idx.repetition(:);
obj.idx.set(1,Nrange) = hdr.idx.set(:);
obj.idx.segment(1,Nrange) = hdr.idx.segment(:);
obj.idx.user(:,Nrange) = hdr.idx.user(:);
obj.user_int(:,Nrange) = hdr.user_int(:);
obj.user_float(:,Nrange) = hdr.user_float(:);
end
function fromStruct(obj, hdr)
% Convert a struct to the object
N = length(hdr.version);
%warning! no error checking
obj.version = reshape(hdr.version,[1,N]);
obj.flags = reshape(hdr.flags,[1,N]);
obj.measurement_uid = reshape(hdr.measurement_uid,[1,N]);
obj.scan_counter = reshape(hdr.scan_counter,[1,N]);
obj.acquisition_time_stamp = reshape(hdr.acquisition_time_stamp,[1,N]);
obj.physiology_time_stamp = reshape(hdr.physiology_time_stamp,[3,N]);
obj.number_of_samples = reshape(hdr.number_of_samples,[1,N]);
obj.available_channels = reshape(hdr.available_channels,[1,N]);
obj.active_channels = reshape(hdr.active_channels,[1,N]);
obj.channel_mask = reshape(hdr.channel_mask,[16,N]);
obj.discard_pre = reshape(hdr.discard_pre,[1,N]);
obj.discard_post = reshape(hdr.discard_post,[1,N]);
obj.center_sample = reshape(hdr.center_sample,[1,N]);
obj.encoding_space_ref = reshape(hdr.encoding_space_ref,[1,N]);
obj.trajectory_dimensions = reshape(hdr.trajectory_dimensions,[1,N]);
obj.sample_time_us = reshape(hdr.sample_time_us,[1,N]);
obj.position = reshape(hdr.position,[3,N]);
obj.read_dir = reshape(hdr.read_dir,[3,N]);
obj.phase_dir = reshape(hdr.phase_dir,[3,N]);
obj.slice_dir = reshape(hdr.slice_dir,[3,N]);
obj.patient_table_position = reshape(hdr.patient_table_position,[3,N]);
obj.idx.kspace_encode_step_1 = reshape(hdr.idx.kspace_encode_step_1,[1,N]);
obj.idx.kspace_encode_step_2 = reshape(hdr.idx.kspace_encode_step_2,[1,N]);
obj.idx.average = reshape(hdr.idx.average,[1,N]);
obj.idx.slice = reshape(hdr.idx.slice,[1,N]);
obj.idx.contrast = reshape(hdr.idx.contrast,[1,N]);
obj.idx.phase = reshape(hdr.idx.phase,[1,N]);
obj.idx.repetition = reshape(hdr.idx.repetition,[1,N]);
obj.idx.set = reshape(hdr.idx.set,[1,N]);
obj.idx.segment = reshape(hdr.idx.segment,[1,N]);
obj.idx.user = reshape(hdr.idx.user,[8,N]);
obj.user_int = reshape(hdr.user_int,[8,N]);
obj.user_float = reshape(hdr.user_float,[8,N]);
end
function hdr = toStruct(obj)
% Convert the object to a plain struct
%warning! no error checking
hdr = struct();
hdr.version = obj.version;
hdr.flags = obj.flags;
hdr.measurement_uid = obj.measurement_uid;
hdr.scan_counter = obj.scan_counter;
hdr.acquisition_time_stamp = obj.acquisition_time_stamp;
hdr.physiology_time_stamp = obj.physiology_time_stamp;
hdr.number_of_samples = obj.number_of_samples;
hdr.available_channels = obj.available_channels;
hdr.active_channels = obj.active_channels;
hdr.channel_mask = obj.channel_mask;
hdr.discard_pre = obj.discard_pre;
hdr.discard_post = obj.discard_post;
hdr.center_sample = obj.center_sample;
hdr.encoding_space_ref = obj.encoding_space_ref;
hdr.trajectory_dimensions = obj.trajectory_dimensions;
hdr.sample_time_us = obj.sample_time_us;
hdr.position = obj.position;
hdr.read_dir = obj.read_dir;
hdr.phase_dir = obj.phase_dir;
hdr.slice_dir = obj.slice_dir;
hdr.patient_table_position = obj.patient_table_position;
hdr.idx.kspace_encode_step_1 = obj.idx.kspace_encode_step_1;
hdr.idx.kspace_encode_step_2 = obj.idx.kspace_encode_step_2;
hdr.idx.average = obj.idx.average;
hdr.idx.slice = obj.idx.slice;
hdr.idx.contrast = obj.idx.contrast;
hdr.idx.phase = obj.idx.phase;
hdr.idx.repetition = obj.idx.repetition;
hdr.idx.set = obj.idx.set;
hdr.idx.segment = obj.idx.segment;
hdr.idx.user = obj.idx.user;
hdr.user_int = obj.user_int;
hdr.user_float = obj.user_float;
end
function fromBytes(obj, bytearray)
% Convert from a byte array to an ISMRMRD AcquisitionHeader
% This conforms to the memory layout of the C-struct
if size(bytearray,1) ~= 340
error('Wrong number of bytes for AcquisitionHeader.')
end
N = size(bytearray,2);
obj.version = reshape(typecast(reshape(bytearray( 1: 2, :), 1, 2 * N), 'uint16'), 1, N); % First unsigned int indicates the version %
obj.flags = reshape(typecast(reshape(bytearray( 3: 10, :), 1, 8 * N), 'uint64'), 1, N); % bit field with flags %
obj.measurement_uid = reshape(typecast(reshape(bytearray( 11: 14, :), 1, 4 * N), 'uint32'), 1, N); % Unique ID for the measurement %
obj.scan_counter = reshape(typecast(reshape(bytearray( 15: 18, :), 1, 4 * N), 'uint32'), 1, N); % Current acquisition number in the measurement %
obj.acquisition_time_stamp = reshape(typecast(reshape(bytearray( 19: 22, :), 1, 4 * N), 'uint32'), 1, N); % Acquisition clock %
obj.physiology_time_stamp = reshape(typecast(reshape(bytearray( 23: 34, :), 1, 4 * 3 * N), 'uint32'), 3, N); % Physiology time stamps, e.g. ecg, breating, etc. %
obj.number_of_samples = reshape(typecast(reshape(bytearray( 35: 36, :), 1, 2 * N), 'uint16'), 1, N); % Number of samples acquired %
obj.available_channels = reshape(typecast(reshape(bytearray( 37: 38, :), 1, 2 * N), 'uint16'), 1, N); % Available coils %
obj.active_channels = reshape(typecast(reshape(bytearray( 39: 40, :), 1, 2 * N), 'uint16'), 1, N); % Active coils on current acquisiton %
obj.channel_mask = reshape(typecast(reshape(bytearray( 41:168, :), 1, 8 * 16 * N), 'uint64'), 16, N); % Mask to indicate which channels are active. Support for 1024 channels %
obj.discard_pre = reshape(typecast(reshape(bytearray( 169:170, :), 1, 2 * N), 'uint16'), 1, N); % Samples to be discarded at the beginning of acquisition %
obj.discard_post = reshape(typecast(reshape(bytearray( 171:172, :), 1, 2 * N), 'uint16'), 1, N); % Samples to be discarded at the end of acquisition %
obj.center_sample = reshape(typecast(reshape(bytearray( 173:174, :), 1, 2 * N), 'uint16'), 1, N); % Sample at the center of k-space %
obj.encoding_space_ref = reshape(typecast(reshape(bytearray( 175:176, :), 1, 2 * N), 'uint16'), 1, N); % Reference to an encoding space, typically only one per acquisition %
obj.trajectory_dimensions = reshape(typecast(reshape(bytearray( 177:178, :), 1, 2 * N), 'uint16'), 1, N); % Indicates the dimensionality of the trajectory vector (0 means no trajectory) %
obj.sample_time_us = reshape(typecast(reshape(bytearray( 179:182, :), 1, 4 * N), 'single'), 1, N); % Time between samples in micro seconds, sampling BW %
obj.position = reshape(typecast(reshape(bytearray( 183:194, :), 1, 4 * 3 * N), 'single'), 3, N); % Three-dimensional spatial offsets from isocenter %
obj.read_dir = reshape(typecast(reshape(bytearray( 195:206, :), 1, 4 * 3 * N), 'single'), 3, N); % Directional cosines of the readout/frequency encoding %
obj.phase_dir = reshape(typecast(reshape(bytearray( 207:218, :), 1, 4 * 3 * N), 'single'), 3, N); % Directional cosines of the phase encoding %
obj.slice_dir = reshape(typecast(reshape(bytearray( 219:230, :), 1, 4 * 3 * N), 'single'), 3, N); % Directional cosines of the slice %
obj.patient_table_position = reshape(typecast(reshape(bytearray( 231:242, :), 1, 4 * 3 * N), 'single'), 3, N); % Patient table off-center %
obj.idx.kspace_encode_step_1 = reshape(typecast(reshape(bytearray( 243:244, :), 1, 2 * N), 'uint16'), 1, N); % phase encoding line number %
obj.idx.kspace_encode_step_2 = reshape(typecast(reshape(bytearray( 245:246, :), 1, 2 * N), 'uint16'), 1, N); % partition encodning number %
obj.idx.average = reshape(typecast(reshape(bytearray( 247:248, :), 1, 2 * N), 'uint16'), 1, N); % signal average number %
obj.idx.slice = reshape(typecast(reshape(bytearray( 249:250, :), 1, 2 * N), 'uint16'), 1, N); % imaging slice number %
obj.idx.contrast = reshape(typecast(reshape(bytearray( 251:252, :), 1, 2 * N), 'uint16'), 1, N); % echo number in multi-echo %
obj.idx.phase = reshape(typecast(reshape(bytearray( 253:254, :), 1, 2 * N), 'uint16'), 1, N); % cardiac phase number %
obj.idx.repetition = reshape(typecast(reshape(bytearray( 255:256, :), 1, 2 * N), 'uint16'), 1, N); % dynamic number for dynamic scanning %
obj.idx.set = reshape(typecast(reshape(bytearray( 257:258, :), 1, 2 * N), 'uint16'), 1, N); % flow encoding set %
obj.idx.segment = reshape(typecast(reshape(bytearray( 259:260, :), 1, 2 * N), 'uint16'), 1, N); % segment number for segmented acquisition %
obj.idx.user = reshape(typecast(reshape(bytearray( 261:276, :), 1, 2 * 8 * N), 'uint16'), 8, N); % Free user parameters %
obj.user_int = reshape(typecast(reshape(bytearray( 277:308, :), 1, 4 * 8 * N), 'int32' ), 8, N); % Free user parameters %
obj.user_float = reshape(typecast(reshape(bytearray( 309:340, :), 1, 4 * 8 * N), 'single'), 8, N); % Free user parameters %
end
function bytes = toBytes(obj)
% Convert to an ISMRMRD AcquisitionHeader to a byte array
% This conforms to the memory layout of the C-struct
N = obj.getNumber;
bytes = zeros(340,N,'uint8');
for p = 1:N
off = 1;
bytes(off:off+1,p) = typecast(obj.version(p) ,'uint8'); off=off+2;
bytes(off:off+7,p) = typecast(obj.flags(p) ,'uint8'); off=off+8;
bytes(off:off+3,p) = typecast(obj.measurement_uid(p) ,'uint8'); off=off+4;
bytes(off:off+3,p) = typecast(obj.scan_counter(p) ,'uint8'); off=off+4;
bytes(off:off+3,p) = typecast(obj.acquisition_time_stamp(p),'uint8'); off=off+4;
bytes(off:off+11,p) = typecast(obj.physiology_time_stamp(:,p) ,'uint8'); off=off+12;
bytes(off:off+1,p) = typecast(obj.number_of_samples(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.available_channels(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.active_channels(p) ,'uint8'); off=off+2;
bytes(off:off+127,p) = typecast(obj.channel_mask(:,p) ,'uint8'); off=off+128;
bytes(off:off+1,p) = typecast(obj.discard_pre(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.discard_post(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.center_sample(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.encoding_space_ref(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.trajectory_dimensions(p) ,'uint8'); off=off+2;
bytes(off:off+3,p) = typecast(obj.sample_time_us(p) ,'uint8'); off=off+4;
bytes(off:off+11,p) = typecast(obj.position(:,p) ,'uint8'); off=off+12;
bytes(off:off+11,p) = typecast(obj.read_dir(:,p) ,'uint8'); off=off+12;
bytes(off:off+11,p) = typecast(obj.phase_dir(:,p) ,'uint8'); off=off+12;
bytes(off:off+11,p) = typecast(obj.slice_dir(:,p) ,'uint8'); off=off+12;
bytes(off:off+11,p) = typecast(obj.patient_table_position(:,p),'uint8'); off=off+12;
bytes(off:off+1,p) = typecast(obj.idx.kspace_encode_step_1(p),'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.kspace_encode_step_2(p),'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.average(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.slice(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.contrast(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.phase(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.repetition(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.set(p) ,'uint8'); off=off+2;
bytes(off:off+1,p) = typecast(obj.idx.segment(p) ,'uint8'); off=off+2;
bytes(off:off+15,p) = typecast(obj.idx.user(:,p) ,'uint8'); off=off+16;
bytes(off:off+31,p) = typecast(obj.user_int(:,p) ,'uint8'); off=off+32;
bytes(off:off+31,p) = typecast(obj.user_float(:,p) ,'uint8');
end
end
function obj = check(obj)
% Check and fix the obj types
% Check the number of elements for each entry
N = obj.getNumber();
if (size(obj.flags) ~= N)
error('Size of flags is not correct.');
end
if ((size(obj.measurement_uid,1) ~= 1) || ...
(size(obj.measurement_uid,2) ~= N))
error('Size of measurement_uid is not correct.');
end
if ((size(obj.scan_counter,1) ~= 1) || ...
(size(obj.scan_counter,2) ~= N))
error('Size of scan_counter is not correct.');
end
if ((size(obj.acquisition_time_stamp,1) ~= 1) || ...
(size(obj.acquisition_time_stamp,2) ~= N))
error('Size of acquisition_time_stamp is not correct.');
end
if ((size(obj.physiology_time_stamp,1) ~= 3) || ...
(size(obj.physiology_time_stamp,2) ~= N))
error('Size of physiology_time_stamp is not correct.');
end
if ((size(obj.number_of_samples,1) ~= 1) || ...
(size(obj.number_of_samples,2) ~= N))
error('Size of number_of_samples is not correct.');
end
if ((size(obj.available_channels,1) ~= 1) || ...
(size(obj.available_channels,2) ~= N))
error('Size of available_channels is not correct.');
end
if ((size(obj.active_channels,1) ~= 1) || ...
(size(obj.active_channels,2) ~= N))
error('Size of active_channels is not correct.');
end
if ((size(obj.channel_mask,1) ~= 16) || ...
(size(obj.channel_mask,2) ~= N))
error('Size of channel_mask is not correct.');
end
if ((size(obj.discard_pre,1) ~= 1) || ...
(size(obj.discard_pre,2) ~= N))
error('Size of discard_pre is not correct.');
end
if ((size(obj.discard_post,1) ~= 1) || ...
(size(obj.discard_post,2) ~= N))
error('Size of discard_post is not correct.');
end
if ((size(obj.center_sample,1) ~= 1) || ...
(size(obj.center_sample,2) ~= N))
error('Size of center_sample is not correct.');
end
if ((size(obj.encoding_space_ref,1) ~= 1) || ...
(size(obj.encoding_space_ref,2) ~= N))
error('Size of encoding_space_ref is not correct.');
end
if ((size(obj.trajectory_dimensions,1) ~= 1) || ...
(size(obj.trajectory_dimensions,2) ~= N))
error('Size of trajectory_dimensions is not correct.');
end
if ((size(obj.sample_time_us,1) ~= 1) || ...
(size(obj.sample_time_us,2) ~= N))
error('Size of sample_time_us is not correct.');
end
if ((size(obj.position,1) ~= 3) || ...
(size(obj.position,2) ~= N))
error('Size of position is not correct.');
end
if ((size(obj.read_dir,1) ~= 3) || ...
(size(obj.read_dir,2) ~= N))
error('Size of read_dir is not correct.');
end
if ((size(obj.phase_dir,1) ~= 3) || ...
(size(obj.phase_dir,2) ~= N))
error('Size of phase_dir is not correct.');
end
if ((size(obj.slice_dir,1) ~= 3) || ...
(size(obj.slice_dir,2) ~= N))
error('Size of slice_dir is not correct.');
end
if ((size(obj.patient_table_position,1) ~= 3) || ...
(size(obj.patient_table_position,2) ~= N))
error('Size of patient_table_position is not correct.');
end
if ((size(obj.idx.kspace_encode_step_1,1) ~= 1) || ...
(size(obj.idx.kspace_encode_step_1,2) ~= N))
error('Size of kspace_encode_step_1 is not correct.');
end
if ((size(obj.idx.kspace_encode_step_2,1) ~= 1) || ...
(size(obj.idx.kspace_encode_step_2,2) ~= N))
error('Size of kspace_encode_step_2 is not correct.');
end
if ((size(obj.idx.average,1) ~= 1) || ...
(size(obj.idx.average,2) ~= N))
error('Size of idx.average is not correct.');
end
if ((size(obj.idx.slice,1) ~= 1) || ...
(size(obj.idx.slice,2) ~= N))
error('Size of idx.slice is not correct.');
end
if ((size(obj.idx.contrast,1) ~= 1) || ...
(size(obj.idx.contrast,2) ~= N))
error('Size of idx.contrast is not correct.');
end
if ((size(obj.idx.phase,1) ~= 1) || ...
(size(obj.idx.phase,2) ~= N))
error('Size of idx.phase is not correct.');
end
if ((size(obj.idx.repetition,1) ~= 1) || ...
(size(obj.idx.repetition,2) ~= N))
error('Size of idx.repetition is not correct.');
end
if ((size(obj.idx.set,1) ~= 1) || ...
(size(obj.idx.set,2) ~= N))
error('Size of idx.set is not correct.');
end
if ((size(obj.idx.segment,1) ~= 1) || ...
(size(obj.idx.segment,2) ~= N))
error('Size of idx.segment is not correct.');
end
if ((size(obj.idx.user,1) ~= 8) || ...
(size(obj.idx.user,2) ~= N))
error('Size of idx.user is not correct.');
end
if ((size(obj.user_int,1) ~= 8) || ...
(size(obj.user_int,2) ~= N))
error('Size of user_int is not correct.');
end
if ((size(obj.user_float,1) ~= 8) || ...
(size(obj.user_float,2) ~= N))
error('Size of user_float is not correct.');
end
% Fix the type of all the elements
obj.version = uint16(obj.version);
obj.flags = uint64(obj.flags);
obj.measurement_uid = uint32(obj.measurement_uid);
obj.scan_counter = uint32(obj.scan_counter);
obj.acquisition_time_stamp = uint32(obj.acquisition_time_stamp);
obj.physiology_time_stamp = uint32(obj.physiology_time_stamp);
obj.number_of_samples = uint16(obj.number_of_samples);
obj.available_channels = uint16(obj.available_channels);
obj.active_channels = uint16(obj.active_channels);
obj.channel_mask = uint64(obj.channel_mask);
obj.discard_pre = uint16(obj.discard_pre);
obj.discard_post = uint16(obj.discard_post);
obj.center_sample = uint16(obj.center_sample);
obj.encoding_space_ref = uint16(obj.encoding_space_ref);
obj.trajectory_dimensions = uint16(obj.trajectory_dimensions);
obj.sample_time_us = single(obj.sample_time_us);
obj.position = single(obj.position);
obj.read_dir = single(obj.read_dir);
obj.phase_dir = single(obj.phase_dir);
obj.slice_dir = single(obj.slice_dir);
obj.patient_table_position = single(obj.patient_table_position);
obj.idx.kspace_encode_step_1 = uint16(obj.idx.kspace_encode_step_1);
obj.idx.kspace_encode_step_2 = uint16(obj.idx.kspace_encode_step_2);
obj.idx.average = uint16(obj.idx.average);
obj.idx.slice = uint16(obj.idx.slice);
obj.idx.contrast = uint16(obj.idx.contrast);
obj.idx.phase = uint16(obj.idx.phase);
obj.idx.repetition = uint16(obj.idx.repetition);
obj.idx.set = uint16(obj.idx.set);
obj.idx.segment = uint16(obj.idx.segment);
obj.idx.user = uint16(obj.idx.user);
obj.user_int = int32(obj.user_int);
obj.user_float = single(obj.user_float);
end
function ret = flagIsSet(obj, flag, range)
% bool = obj.flagIsSet(flag, range)
if nargin < 3
range = 1:obj.getNumber;
end
if isa(flag, 'char')
b = obj.FLAGS.(flag);
elseif (flag>0)
b = uint64(flag);
else
error('Flag is of the wrong type.');
end
bitmask = bitshift(uint64(1),(b-1));
ret = zeros(size(range));
for p = 1:length(range)
ret(p) = (bitand(obj.flags(range(p)), bitmask)>0);
end
end
function flagSet(obj, flag, range)
if nargin < 3
range = 1:obj.getNumber;
end
if isa(flag, 'char')
b = obj.FLAGS.(flag);
elseif (flag>0)
b = uint64(flag);
else
error('Flag is of the wrong type.');
end
bitmask = bitshift(uint64(1),(b-1));
alreadyset = obj.flagIsSet(flag,range);
for p = 1:length(range)
if ~alreadyset(p)
obj.flags(range(p)) = obj.flags(range(p)) + bitmask;
end
end
end
function flagClear(obj, flag, range)
if nargin < 3
range = 1:obj.getNumber;
end
if isa(flag, 'char')
b = obj.FLAGS.(flag);
elseif (flag>0)
b = uint64(flag);
else
error('Flag is of the wrong type.');
end
bitmask = bitshift(uint64(1),(b-1));
alreadyset = obj.flagIsSet(flag,range);
for p = 1:length(range)
if alreadyset(p)
obj.flags(range(p)) = obj.flags(range(p)) - bitmask;
end
end
end
function flagClearAll(obj, range)
if nargin < 2
range = 1:obj.getNumber;
end
obj.flags(range) = zeros(1,length(range),'uint64');
end
end
end
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