/
twix_map_obj_fire.m
204 lines (187 loc) · 8.38 KB
/
twix_map_obj_fire.m
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classdef twix_map_obj_fire < handle %matlab.mixin.Copyable %handle
properties
% flagRemoveOS: 0
% flagDoAverage: 0
% flagAverageReps: 0
% flagAverageSets: 0
flagIgnoreSeg = true;
% flagSkipToFirstLine: 0
% flagRampSampRegrid: 0
% flagDoRawDataCorrect: 0
% RawDataCorrectionFactors: []
% filename: '/Users/kelvin/Downloads/tmp.dat'
% dataType: 'image'
% softwareVersion: 'vd'
dataSize = ones(1,16);
dataDims = {'Col' 'Cha' 'Lin' 'Par' 'Sli' 'Ave' 'Phs' 'Eco' 'Rep' 'Set' 'Seg' 'Ida' 'Idb' 'Idc' 'Idd' 'Ide'};
sqzSize = [];
sqzDims = {};
NCol
NCha
NLin
NPar
NSli
NAve
NPhs
NEco
NRep
NSet
NSeg
NIda
NIdb
NIdc
NIdd
NIde
NAcq
Lin
Par
Sli
Ave
Phs
Eco
Rep
Set
Seg
Ida
Idb
Idc
Idd
Ide
centerCol
centerLin
centerPar
cutOff
% coilSelect: [1�12180 double]
% ROoffcenter: [1�12180 double]
timeSinceRF
% IsReflected: [1�12180 logical]
% IsRawDataCorrect: [1�12180 logical]
slicePos
% freeParam: [4�12180 double]
iceParam
scancounter
timestamp
pmutime
% rampSampTrj: []
% memPos: [1�12180 double]
% evalInfo1: [1�12180 double]
% evalInfo2: [1�12180 double]
% ixToTarget: [1�12180 double]
% ixToRaw: [1�24150 double]
% isBrokenFile: 0
mrdAcq
end
methods
function raw = imageData(obj)
if obj.flagIgnoreSeg
NSegUsed = 1;
else
NSegUsed = obj.NSeg;
end
raw = zeros(obj.NCol, ...
obj.NCha, ...
obj.NLin, ...
obj.NPar, ...
obj.NSli, ...
obj.NAve, ...
obj.NPhs, ...
obj.NEco, ...
obj.NRep, ...
obj.NSet, ...
NSegUsed, ...
obj.NIda, ...
obj.NIdb, ...
obj.NIdc, ...
obj.NIdd, ...
obj.NIde, 'like', complex(single(0)));
for iRO = 1:numel(obj.mrdAcq)
if obj.flagIgnoreSeg
SegUsed = 1;
else
SegUsed = obj.Seg(iRO);
end
raw(:, ... % 1: Col
:, ... % 2: Cha
obj.Lin(iRO), ... % 3: Lin
obj.Par(iRO), ... % 4: Par
obj.Sli(iRO), ... % 5: Sli
obj.Ave(iRO), ... % 6: Ave
obj.Phs(iRO), ... % 7: Phs
obj.Eco(iRO), ... % 8: Eco
obj.Rep(iRO), ... % 9: Rep
obj.Set(iRO), ... % 10: Set
SegUsed, ... % 11: Seg
obj.Ida(iRO), ... % 12: Ida
obj.Idb(iRO), ... % 13: Idb
obj.Idc(iRO), ... % 14: Idc
obj.Idd(iRO), ... % 15: Idd
obj.Ide(iRO)) ... % 16: Ide
= obj.mrdAcq{iRO}.data;
end
end
% Return all k-space data without sorting [RO Cha Lin]
function ksp = unsorted(obj)
ksp = cell2mat(permute(cellfun(@(x) x.data, obj.mrdAcq, 'UniformOutput', false), [1 3 2]));
end
function obj = setMrdAcq(obj, mrdAcq)
obj.mrdAcq = mrdAcq;
% Determine whic
% .image: image scan
% .noise: for noise scan
% .phasecor: phase correction scan
% .phasestab: phase stabilization scan
% .phasestabRef0: phase stab. ref. (MDH_REFPHASESTABSCAN && !MDH_PHASESTABSCAN)
% .phasestabRef1: phase stab. ref. (MDH_REFPHASESTABSCAN && MDH_PHASESTABSCAN)
% .refscan: parallel imaging reference scan
% Loop indices for each (unsorted) line
obj.Lin = cellfun(@(x) x.head.idx.kspace_encode_step_1, mrdAcq) + 1;
obj.Par = cellfun(@(x) x.head.idx.kspace_encode_step_2, mrdAcq) + 1;
obj.Sli = cellfun(@(x) x.head.idx.slice, mrdAcq) + 1;
obj.Ave = cellfun(@(x) x.head.idx.average, mrdAcq) + 1;
obj.Phs = cellfun(@(x) x.head.idx.phase, mrdAcq) + 1;
obj.Eco = cellfun(@(x) x.head.idx.contrast, mrdAcq) + 1;
obj.Rep = cellfun(@(x) x.head.idx.repetition, mrdAcq) + 1;
obj.Set = cellfun(@(x) x.head.idx.set, mrdAcq) + 1;
obj.Seg = cellfun(@(x) x.head.idx.segment, mrdAcq) + 1;
obj.Ida = cellfun(@(x) x.head.idx.user(1), mrdAcq) + 1;
obj.Idb = cellfun(@(x) x.head.idx.user(2), mrdAcq) + 1;
obj.Idc = cellfun(@(x) x.head.idx.user(3), mrdAcq) + 1;
obj.Idd = cellfun(@(x) x.head.idx.user(4), mrdAcq) + 1;
obj.Ide = cellfun(@(x) x.head.idx.user(5), mrdAcq) + 1;
obj.scancounter = cellfun(@(x) x.head.scan_counter, mrdAcq);
obj.timestamp = cellfun(@(x) x.head.acquisition_time_stamp, mrdAcq);
obj.pmutime = cell2mat(cellfun(@(x) x.head.physiology_time_stamp', mrdAcq, 'UniformOutput', false));
obj.centerCol = cellfun(@(x) x.head.center_sample, mrdAcq) + 1;
obj.centerLin = cellfun(@(x) x.head.idx.user(6), mrdAcq) + 1;
obj.centerPar = cellfun(@(x) x.head.idx.user(7), mrdAcq) + 1;
obj.timeSinceRF = cellfun(@(x) x.head.user_int(8), mrdAcq);
obj.cutOff = cell2mat(cellfun(@(x) [x.head.discard_pre; x.head.discard_post], mrdAcq, 'UniformOutput', false));
% TODO: last 4 rows are the the quaternion, which need to be converted from the slice directions
obj.slicePos = cell2mat(cellfun(@(x) x.head.position, mrdAcq, 'UniformOutput', false)');
obj.iceParam = zeros(24, numel(mrdAcq));
obj.iceParam(1:7, :) = cell2mat(cellfun(@(x) x.head.user_int(1:7), mrdAcq, 'UniformOutput', false)')'; % Parameter 8 (1-indexed) is not converted :/
obj.iceParam(9:16,:) = cell2mat(cellfun(@(x) x.head.user_float, mrdAcq, 'UniformOutput', false)')';
% Maximum size of each dimension
obj.NCol = size( obj.mrdAcq{1}.data,1); % Assuming that all readouts have the same size
obj.NCha = size( obj.mrdAcq{1}.data,2); % Assuming that all readouts have the same number of coils
obj.NLin = max( obj.Lin);
obj.NPar = max( obj.Par);
obj.NSli = max( obj.Sli);
obj.NAve = max( obj.Ave);
obj.NPhs = max( obj.Phs);
obj.NEco = max( obj.Eco);
obj.NRep = max( obj.Rep);
obj.NSet = max( obj.Set);
obj.NSeg = max( obj.Seg);
obj.NIda = max( obj.Ida);
obj.NIdb = max( obj.Idb);
obj.NIdc = max( obj.Idc);
obj.NIdd = max( obj.Idd);
obj.NIde = max( obj.Ide);
obj.NAcq = numel(obj.mrdAcq);
obj.dataSize = [obj.NCol obj.NCha obj.NLin obj.NPar obj.NSli obj.NAve obj.NPhs obj.NEco obj.NRep obj.NSet obj.NSeg obj.NIda obj.NIdb obj.NIdc obj.NIdd obj.NIde];
obj.sqzSize = obj.dataSize(obj.dataSize ~= 1);
obj.sqzDims = obj.dataDims(obj.dataSize ~= 1);
end
end
end