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MauroLeidiMauroLeidi
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bugfix, rawdata reader display steady state wrong because of assumed nshot nseg too early
1 parent 5259878 commit 1c5a549

6 files changed

Lines changed: 227 additions & 27 deletions

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src/ISMRMRD/checkMetadataInteractive.m renamed to src/rawDataReader/checkMetadataInteractive.m

File renamed without changes.

‎src/rawDataReader/correctMetadataInteractive.m‎

Lines changed: 178 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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function [myMriAcquisition_node, reconFoV] = correctMetadataInteractive(myMriAcquisition_node, reconFoV)
2+
%CORRECTMETADATAINTERACTIVE
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% Opens the metadata editing window for user correction.
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% Standalone version — only displays the parameter table.
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%
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% Authors:
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% Dominik Helbing
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% adapted and simplified by Mauro Leidi, 2024
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%
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% -------------------------------------------------------------------------
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%% --- Input check -----------------------------------------------------
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if ~isa(myMriAcquisition_node, 'bmMriAcquisitionParam')
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error("First argument must be an object of class bmMriAcquisitionParam.");
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end
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%% --- Parameter setup -------------------------------------------------
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paramNames = {'N', 'nLine', 'nShot', 'nSeg', 'nCh', 'nEcho', ...
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'nShotOff', 'FoV (acq)', 'FoV (recon)'};
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21+
automatedValues = [myMriAcquisition_node.N, ...
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myMriAcquisition_node.nLine, ...
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myMriAcquisition_node.nShot, ...
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myMriAcquisition_node.nSeg, ...
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myMriAcquisition_node.nCh, ...
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myMriAcquisition_node.nEcho, ...
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myMriAcquisition_node.nShot_off, ...
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mode(myMriAcquisition_node.FoV), ...
29+
mode(reconFoV)];
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%% --- Create main UI figure ------------------------------------------
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fig = uifigure('Name', 'Manual Parameter Adjustment', ...
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'Position', [100 100 650 285]);
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movegui(fig, 'center');
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36+
g = uigridlayout(fig, ...
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'RowHeight', {'fit','fit','1x'}, ...
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'ColumnWidth', {'1x','fit'});
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g2 = uigridlayout(g, [5,1], ...
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'RowHeight', {'fit', 'fit', 'fit', 30, 30});
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g2.Layout.Row = 2;
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g2.Layout.Column = 2;
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% Title label
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t = uilabel(g, ...
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'Text', 'Adjust Acquisition Parameters', ...
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'FontSize', 14, ...
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'FontWeight', 'bold', ...
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'HorizontalAlignment', 'center');
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t.Layout.Row = 1;
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t.Layout.Column = [1,2];
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%% --- Table -----------------------------------------------------------
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s = uistyle('BackgroundColor', [0.9290 0.6940 0.1250]); % orange highlight
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data = [paramNames', num2cell(automatedValues)', num2cell(automatedValues)'];
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58+
uit = uitable(g, ...
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'Data', data, ...
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'ColumnEditable', [false false true], ...
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'ColumnName', {'Acquisition Parameters', 'Extracted Value', 'User Value'}, ...
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'ColumnWidth', '1x');
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uit.Layout.Row = 2;
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uit.Layout.Column = 1;
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addStyle(uit, s, "column", 3);
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%% --- Controls (dropdowns, checkbox, buttons) -------------------------
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% Add dropdown for different cases, maybe table changes depending on case
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dd = uidropdown(g2, 'Items', {'Non-Cartesian', 'Cartesian', 'Case 3'}, ...
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"ValueChangedFcn",@(src,event) updateTable(src, uit));
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dropDown = dd.Value;
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% Add dropdown for navigation
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dd_self = uidropdown(g2, 'Items', {'SI Navigation', ...
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'Pilot Tone Navigation', ...
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'Other'});
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% If self nav is not used atm
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if ~myMriAcquisition_node.selfNav_flag
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dd_self.Value = 'Other';
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end
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83+
% Add a checkbox for roosk_flag
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cbx_rooks = uicheckbox(g2, 'Text', 'Remove oversampling', 'Value', ...
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myMriAcquisition_node.roosk_flag);
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87+
% Add a button to confirm changes
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uibutton(g2, 'Text', 'Confirm', ...
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'ButtonPushedFcn', @(btn,event) confirmCallback(fig));
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% Add a button to cancel
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uibutton(g2, 'Text', 'Cancel', 'BackgroundColor', '#d0d0d0', ...
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'ButtonPushedFcn', @(btn,event) closeFigure(fig));
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% Handle figure close request to resume execution
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fig.CloseRequestFcn = @(src, event) closeFigure(fig);
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%% --- Wait for user interaction --------------------------------------
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uiwait(fig);
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%% --- Retrieve values after closing ----------------------------------
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% Only update the values if figure was closed using "Confirm"
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if ishandle(fig)
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% Table values
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automatedValues = cell2mat(uit.Data(:,3))';
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% Checkbox values
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selfNav = strcmp(dd_self.Value, 'SI Navigation');
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myMriAcquisition_node.selfNav_flag = selfNav;
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myMriAcquisition_node.roosk_flag = cbx_rooks.Value;
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113+
% Dropdown value
114+
dropDown = dd.Value;
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116+
% Close the figure
117+
close(fig);
118+
end
119+
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%% Return values
121+
% Update values in myMriAcquisition_node
122+
if strcmp(dropDown, 'Non-Cartesian')
123+
% Table values
124+
myMriAcquisition_node.N = automatedValues(1);
125+
myMriAcquisition_node.nLine = automatedValues(2);
126+
myMriAcquisition_node.nShot = automatedValues(3);
127+
myMriAcquisition_node.nSeg = automatedValues(4);
128+
myMriAcquisition_node.nCh = automatedValues(5);
129+
myMriAcquisition_node.nEcho = automatedValues(6);
130+
myMriAcquisition_node.nShot_off = automatedValues(7);
131+
newFoV = ones(size(myMriAcquisition_node.FoV)).*automatedValues(8);
132+
myMriAcquisition_node.FoV = newFoV;
133+
reconFoV = ones(size(myMriAcquisition_node.FoV)).*automatedValues(9);
134+
end
135+
136+
if strcmp(dropDown, 'Cartesian')
137+
error("Case not implemented yet");
138+
end
139+
140+
if strcmp(dropDown, 'Case 3')
141+
error("Case not implemented yet");
142+
end
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% End of function
144+
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%% --- Nested callback functions --------------------------------------
146+
function confirmCallback(fig)
147+
uiresume(fig);
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end
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150+
function updateTable(src, uit)
151+
% Callback function to handle a dropdown change NOT IN USE YET
152+
% Change the background color of the columns depending on the drop
153+
% down. This is only as an example on how to use it.
154+
cols = uistyle('BackgroundColor', [0.9290 0.6940 0.1250]);
155+
removeStyle(uit);
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switch src.Value
157+
case 'Non-Cartesian'
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col = 3;
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case 'Cartesian'
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col = 2;
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case 'Case 3'
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col = 1;
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otherwise
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col = 1;
165+
end
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addStyle(uit, cols, "column", col);
167+
end
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function closeFigure(fig)
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% Callback function to handle figure close event
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% Resume execution and close the figure
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uiresume(fig);
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delete(fig);
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end
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end

src/ISMRMRD/ISMRMRD_readParam.m renamed to src/rawDataReader/ismrmrd/ISMRMRD_readParam.m

File renamed without changes.

src/ISMRMRD/bmISMRMRD_data.m renamed to src/rawDataReader/ismrmrd/bmISMRMRD_data.m

File renamed without changes.

‎src/rawDataReader/siemens/dhSiemensReadMetaData.m‎

Lines changed: 32 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -77,26 +77,51 @@
7777
end
7878
end
7979

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81+
myMriAcquisition_node = bmMriAcquisitionParam([]);
82+
myMriAcquisition_node.N = N;
83+
myMriAcquisition_node.nLine = nLine;
84+
myMriAcquisition_node.nShot = nShot;
85+
myMriAcquisition_node.nSeg = nSeg;
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myMriAcquisition_node.nCh = 1;
87+
myMriAcquisition_node.nEcho = nEcho;
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myMriAcquisition_node.FoV = FoV;
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myMriAcquisition_node.timestamp = timestamp;
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reconFoV = FoV;
91+
% Find the shot where the standard deviation falls below the threshold
92+
myMriAcquisition_node.nShot_off = 0;
93+
94+
%% Set flags in myMriAcquisition_node (Maybe other way to handle them?)
95+
myMriAcquisition_node.selfNav_flag = true;
96+
myMriAcquisition_node.roosk_flag = false;
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98+
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%% HERE STEP ONE: LET THE USER CORRECT THE AUTOMATICALLY EXTRACTED METADATA
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if ~autoFlag || isequal(reconFoV, [-1, -1, -1])
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[myMriAcquisition_node, reconFoV] = correctMetadataInteractive(myMriAcquisition_node, reconFoV);
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end
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80105
% unsorted() returns the unsorted data as an array [N, nCh, nLine]
81-
y_raw = myTwix.image.unsorted();
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y_raw = myTwix.image.unsorted(); % this is [N, nCh, nLine]
82107

83108
if nEcho == 1
84109
% Change structure to [nCh, N, nLine] and seperate nLine into nSeg and
85110
% nShot
86-
y_raw = permute(y_raw, [2, 1, 3]);
111+
y_raw = permute(y_raw, [2, 1, 3]); % [nCh, N, nLine]
87112
% Get nCh
88113
y_raw_size = size(y_raw);
89114
y_raw_size = y_raw_size(:)';
90-
nCh = y_raw_size(1, 1);
91-
y_raw = reshape(y_raw, [nCh, N, nSeg, nShot]);
115+
myMriAcquisition_node.nCh = y_raw_size(1, 1);
116+
y_raw = reshape(y_raw, [myMriAcquisition_node.nCh, myMriAcquisition_node.N, myMriAcquisition_node.nSeg, myMriAcquisition_node.nShot]); % [nCh, N, nSeg, nShot]
92117
else
93118
error('bmTwix_data : nEcho > 1, case not implemented, yet ');
94119
end
95120

96121

97122
% Reduce the array to a 3D array, only containing the values for the first
98123
% segment
99-
mySI = squeeze(y_raw(:, :, 1, :));
124+
mySI = squeeze(y_raw(:, :, 1, :)); % [nCh, N, nShot]
100125

101126
% Calculate the inverse discret Fourier transform
102127
mySI = bmIDF(mySI, 1, [], 2);
@@ -127,27 +152,10 @@
127152
running_std = movstd(s_mean, window_size, 'Endpoints', 'discard');
128153

129154
% Define a threshold for the std to consider steady state
130-
threshold = prctile(running_std, 15); % 10th percentile of std
131-
%% Extract acquisition parameters
132-
% Node for trajectory
133-
myMriAcquisition_node = bmMriAcquisitionParam([]);
134-
myMriAcquisition_node.N = N;
135-
myMriAcquisition_node.nLine = nLine;
136-
myMriAcquisition_node.nShot = nShot;
137-
myMriAcquisition_node.nSeg = nSeg;
138-
myMriAcquisition_node.nCh = nCh;
139-
myMriAcquisition_node.nEcho = nEcho;
140-
myMriAcquisition_node.FoV = FoV;
141-
myMriAcquisition_node.timestamp = timestamp;
155+
threshold = prctile(running_std, 15); % 15th percentile of std
156+
142157
% Find the shot where the standard deviation falls below the threshold
143158
myMriAcquisition_node.nShot_off = find(running_std < threshold, 1);
144-
145-
%% Set flags in myMriAcquisition_node (Maybe other way to handle them?)
146-
myMriAcquisition_node.selfNav_flag = true;
147-
myMriAcquisition_node.roosk_flag = false;
148-
149-
150-
reconFoV = FoV;
151159

152160
if ~autoFlag || isequal(reconFoV, [-1, -1, -1])
153161
[myMriAcquisition_node, reconFoV] = checkMetadataInteractive(mySI, s_mean, ...
@@ -164,4 +172,3 @@
164172
end
165173

166174
end
167-

‎src/rawDataReader/siemens/mleSiemensReader.m‎

Lines changed: 17 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,8 +18,23 @@
1818
% getRedouts: extract the readouts, returns a complex array
1919
% containing the data
2020
function rawdata = readRawData(obj, flagSS, flagExcludeSI)
21-
% Handle default values for optional arguments: if no argument
22-
% is passed there is no data filtering.
21+
%READRAWDATA Read raw data with optional filtering.
22+
%
23+
% rawdata = readRawData(obj)
24+
% rawdata = readRawData(obj, flagSS)
25+
% rawdata = readRawData(obj, flagSS, flagExcludeSI)
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%
27+
% INPUTS:
28+
% obj - Reader object containing acquisition parameters
29+
% and the raw file handle.
30+
%
31+
% flagSS - (logical, optional) If true, the initial
32+
% non–steady-state readouts are filtered out.
33+
% Default = false.
34+
%
35+
% flagExcludeSI - (logical, optional) If true, the SI projection
36+
% readouts (self-navigation lines) are excluded
37+
% from the output. Default = false.
2338
if nargin < 2
2439
flagSS = false; % If true the non steady state readouts are filtered out
2540
end

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