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ideacmdtool with XA30 - different recording start & stop times for cardiac and respiratory signals #234

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ideacmdtool with XA30 - different recording start & stop times for cardiac and respiratory signals #234

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5c48e47
Update tapas_physio_read_physlogfiles_siemens.m
alexsayal May 4, 2023
43677d4
Allow separate BIDS files with the same sampling frequency but differ…
alexsayal May 4, 2023
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9 changes: 8 additions & 1 deletion PhysIO/code/readin/tapas_physio_read_columnar_textfiles.m
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,10 @@
strColumnHeader = '';
parsePatternPerNColumns{3} = '%f %f %f';
nEmptyLinesAfterHeader(3) = 0;
case 'BIDS_SEPARATE'
strColumnHeader = '';
parsePatternPerNColumns{1} = '%f';
nEmptyLinesAfterHeader(1) = 0;
case 'BIOPAC_TXT'
strColumnHeader = '.*RESP.*';
parsePatternPerNColumns{4} = '%f %f %f %d';
Expand Down Expand Up @@ -132,6 +136,9 @@
case 'BIDS' % will be in separate json-file
columnNames = {};
nColumns = 3;
case 'BIDS_SEPARATE' % will be in separate json-file
columnNames = {};
nColumns = 1;
case 'BIOPAC_TXT' % bad column names with spaces...e.g. 'RESP - RSP100C'
columnNames = regexp(strLine, '([\t])', 'split');
nColumns = numel(columnNames);
Expand All @@ -151,7 +158,7 @@
% now read the rest of the file
fid = fopen(fileName);
switch upper(fileType)
case {'ADINSTRUMENTS_TXT', 'LABCHART_TXT', 'BIDS', 'BIOPAC_TXT', 'INFO', 'PULS', 'RESP'}
case {'ADINSTRUMENTS_TXT', 'LABCHART_TXT', 'BIDS', 'BIDS_SEPARATE', 'BIOPAC_TXT', 'INFO', 'PULS', 'RESP'}
C = textscan(fid, parsePatternPerNColumns{nColumns}, 'HeaderLines', nHeaderLines);
case 'PHILIPS' % sometimes odd lines with single # occur within text file
C = textscan(fid, parsePatternPerNColumns{nColumns}, 'HeaderLines', nHeaderLines, 'CommentStyle', '#');
Expand Down
91 changes: 80 additions & 11 deletions PhysIO/code/readin/tapas_physio_read_physlogfiles_bids.m
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@
fileName{2} = log_files.respiration;

[c,r,t,cpulse,acq_codes] = tapas_physio_read_physlogfiles_bids_separate(fileName,log_files,hasExplicitJsonFile,DEBUG,verbose);

elseif hasCardiacFile
fileName = log_files.cardiac;
[c,r,t,cpulse,acq_codes] = tapas_physio_read_physlogfiles_bids_unified(fileName,log_files,hasExplicitJsonFile,DEBUG,verbose);
Expand All @@ -97,6 +97,12 @@
[c,r,t,cpulse,acq_codes] = tapas_physio_read_physlogfiles_bids_unified(fileName,log_files,hasExplicitJsonFile,DEBUG,verbose);
end

% De-mean data
c_mean = mean(c);
r_mean = mean(r);
c = c - c_mean;
r = r - r_mean;

end

%% Function for separate physio files (cardiac and resp with different sampling rates)
Expand Down Expand Up @@ -147,7 +153,7 @@
if hasJsonFile
% in BIDS, start of the phys logging is stated relative to the first volume scan start.
% PhysIO defines the scan acquisiton relative to the phys log start
tRelStartScan = -val.StartTime;
tRelStartScanCardiac = -val.StartTime;
else
verbose = tapas_physio_log(...
['No .json file found and empty log_files.relative_start_acquisition. ' ...
Expand All @@ -156,9 +162,9 @@
else
if hasJsonFile
% add both delays
tRelStartScan = log_files.relative_start_acquisition - val.StartTime;
tRelStartScanCardiac = log_files.relative_start_acquisition - val.StartTime;
else
tRelStartScan = log_files.relative_start_acquisition;
tRelStartScanCardiac = log_files.relative_start_acquisition;
end
end

Expand All @@ -175,9 +181,13 @@
end
end

C = tapas_physio_read_columnar_textfiles(fileNameCardiac, 'BIDS');
C = tapas_physio_read_columnar_textfiles(fileNameCardiac, 'BIDS_SEPARATE');
c = double(C{idxCol(1)});
iAcqStart = (double(C{idxCol(2)})~=0); % trigger has 1, rest is 0;
try
iAcqStart = (double(C{idxCol(2)})~=0); % trigger has 1, rest is 0;
catch
iAcqStart = [];
end

%% delete temporary unzipped file
if isZipped
Expand Down Expand Up @@ -228,6 +238,26 @@
end
end

% sum implicit (.json) and explicit relative shifts of log/scan acquisition
if isempty(log_files.relative_start_acquisition)
if hasJsonFile
% in BIDS, start of the phys logging is stated relative to the first volume scan start.
% PhysIO defines the scan acquisiton relative to the phys log start
tRelStartScanRespiratory = -val.StartTime;
else
verbose = tapas_physio_log(...
['No .json file found and empty log_files.relative_start_acquisition. ' ...
'Please specify explicitly.'], verbose, 2);
end
else
if hasJsonFile
% add both delays
tRelStartScanRespiratory = log_files.relative_start_acquisition - val.StartTime;
else
tRelStartScanRespiratory = log_files.relative_start_acquisition;
end
end

% default columns in text file for phys recordings; overruled by JSON file
% 1 = resp, 2 = trigger
bidsColumnNamesRespiration = {'respiratory', 'trigger'};
Expand All @@ -248,8 +278,8 @@
nSamplesCardiac = length(c);
nSamplesRespiration = length(r);

tCardiac = -tRelStartScan + ((0:(nSamplesCardiac-1))*dtCardiac)';
tRespiration = -tRelStartScan + ((0:(nSamplesRespiration-1))*dtRespiration)';
tCardiac = -tRelStartScanCardiac + ((0:(nSamplesCardiac-1))*dtCardiac)';
tRespiration = -tRelStartScanRespiratory + ((0:(nSamplesRespiration-1))*dtRespiration)';

%% Deal with NaNs in c and r timecourse
c(isnan(c)) = interp1(tCardiac(~isnan(c)), c(~isnan(c)), tCardiac(isnan(c)));
Expand All @@ -272,7 +302,9 @@
%dtRespiration = tRespiration(2) - tRespiration(1);

isHigherSamplingCardiac = dtCardiac < dtRespiration;
if isHigherSamplingCardiac
isSameSamplingDiffNSamples = (dtCardiac == dtRespiration) && (nSamplesCardiac ~= nSamplesRespiration);

if isHigherSamplingCardiac && ~isSameSamplingDiffNSamples
t = tCardiac;
rInterp = interp1(tRespiration, r, t);
%racq_codesInterp = interp1(tRespiration, racq_codes, t, 'nearest');
Expand All @@ -285,7 +317,7 @@
end
r = rInterp;

else
elseif ~isHigherSamplingCardiac && ~isSameSamplingDiffNSamples
t = tRespiration;
cInterp = interp1(tCardiac, c, t);
%cacq_codesInterp = interp1(tCardiac, cacq_codes, t, 'nearest');
Expand All @@ -297,7 +329,44 @@
verbose.fig_handles(end+1) = fh;
end
c = cInterp;


elseif isSameSamplingDiffNSamples
% first we must syncronize the time vectors
if tRespiration(1) < tCardiac(1)

[~, indexOfMin] = min(abs(tRespiration-tCardiac(1)));

tRespiration = tRespiration(indexOfMin:end);
r = r(indexOfMin:end);
nSamplesRespiration = length(r);

else

[~, indexOfMin] = min(abs(tCardiac-tRespiration(1)));

tCardiac = tCardiac(indexOfMin:end);
c = c(indexOfMin:end);
nSamplesCardiac = length(c);

end

% % then fill the shorter file with zeros
% if nSamplesRespiration < nSamplesCardiac
% t = tCardiac;
% r(nSamplesRespiration+1:nSamplesCardiac) = 0;
% else
% t = tRespiration;
% c(nSamplesCardiac+1:nSamplesRespiration) = 0;
% end

% then trim the longer file
if nSamplesCardiac > nSamplesRespiration
c = c(1:nSamplesRespiration);
t = tRespiration;
else
r = r(1:nSamplesCardiac);
t = tCardiac;
end
end

%% Recompute acq_codes as for Siemens (volume on/volume off)
Expand Down
35 changes: 31 additions & 4 deletions PhysIO/code/readin/tapas_physio_read_physlogfiles_siemens.m
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -171,9 +171,9 @@

if isempty(dt)
nSamplesC = size(data_table,1);
dt_c = tLogTotal/(nSamplesC-1);
dt_c = round(tLogTotal/(nSamplesC-1), 4);
else
dt_c = dt(1);
dt_c = round(dt(1), 4);
end

dataCardiac = tapas_physio_siemens_table2cardiac(data_table, ecgChannel, dt_c, ...
Expand Down Expand Up @@ -241,9 +241,9 @@

if isempty(dt)
nSamplesR = size(data_table,1);
dt_r = tLogTotal/(nSamplesR-1);
dt_r = round(tLogTotal/(nSamplesR-1), 4);
else
dt_r = dt(end);
dt_r = round(dt(end), 4);
end

dataResp = tapas_physio_siemens_table2cardiac(data_table, ecgChannel, ...
Expand All @@ -270,6 +270,33 @@
t_r = [];
end

%% As the start times of both signal recordings might be different, we should syncronize them before padding
nSamplesR = numel(r);
nSamplesC = numel(c);

isSameSamplingDiffNSamples = (dt_c == dt_r) && (nSamplesC ~= nSamplesR);

if isSameSamplingDiffNSamples

% first we must syncronize the time vectors
if t_r(1) < t_c(1)

[~, indexOfMin] = min(abs(t_r-t_c(1)));

t_r = t_r(indexOfMin:end);
r = r(indexOfMin:end);
nSamplesR = length(r);

else

[~, indexOfMin] = min(abs(t_c-t_r(1)));

t_c = t_c(indexOfMin:end);
c = c(indexOfMin:end);
nSamplesC = length(c);

end
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Adapt time scales resp/cardiac, i.e. zero fill c or r
Expand Down