likeajumprope · likeajumprope · May 17, 2022 · Jul 30, 2022 · Aug 6, 2022 · Aug 10, 2022
diff --git a/.gitignore b/.gitignore
@@ -18,6 +18,7 @@ lib
 .idea
 .idea/*
 examples
+.MATLABDriveTag
 
 # Python
 # See e.g. https://github.com/github/gitignore/blob/master/Python.gitignore

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,20 @@
 # Changelog
 TAPAS toolbox 
+## [6.1.0] 2022-11-18
+### Added 
+- Added `tapas_test` testing function. Started progressive introduction of testing framework.
+- PhysIO [Version 8.2.0](PhysIO/CHANGELOG.md)
+    - Interface `tapas_physio_test` to TAPAS-generic `tapas_test` function
+    - Added suport for logfile version 3 of Siemens physio recordings 
+        - multi ECG/Resp channels and interleaved status messages
+        - new integration test for Siemens VB Logversion 3
+### Fixed
+- PhysIO [Version 8.2.0](PhysIO/CHANGELOG.md)
+    - Removed dependence on `nanmean` (Statistics Toolbox)
+        - See [GitHub issue #205](https://github.com/translationalneuromodeling/tapas/issues/205) 
+    - Compatibility with multiple SPM toolbox locations for `lmod` ([GitHub issue #211](https://github.com/translationalneuromodeling/tapas/issues/211))
+        - as listed in `spm_get_defaults('tbx')`
+    - Refactoring of Philips read-in to support novel 12-column logfile version, see [GitHub issue #207](https://github.com/translationalneuromodeling/tapas/issues/207#issuecomment-1246078600)
 
 ## [6.0.1] 2022-05-17
 
@@ -11,7 +26,7 @@ For this major release of TAPAS, we have decided to move currently unmaintained
 to a dedicated [TAPAS Legacy repository](https://github.com/translationalneuromodeling/tapas_legacy).
 
 ### Added
-- PhysIO [Version 8.1.0](Physio/CHANGELOG.md): BIDS Read-in for separate cardiac/respiratory trace files (e.g., due to different sampling frequencies)
+- PhysIO [Version 8.1.0](PhysIO/CHANGELOG.md): BIDS Read-in for separate cardiac/respiratory trace files (e.g., due to different sampling frequencies)
     - Compatibility of whole code base with Matlab compiler in order to run `spm_make_standalone`.
 ### Changed 
 - Moved `MICP`,`VBLM`,`h2gf` and `mpdcm` toolboxes to TAPAS Legacy repository.

diff --git a/Contributor-License-Agreement.md b/Contributor-License-Agreement.md
@@ -21,6 +21,7 @@ Stephan Heunis           | Eindhoven University of Technology | Eindhoven | NL
 Niklas Bürgi             | SNS, University of Zurich          | Zurich    | CH      | nbuergi                | 1.0
 Alexandre Sayal          | CIBIT, University of Coimbra       | Coimbra   | PT      | alexsayal              | 1.0
 Matthias Müller-Schrader | TNU, University of Zurich          | Zurich    | CH      | mms-neuro              | 1.1
+Johanna M. M. Bayer      | The University of Melbourne        | Melbourne | AU      | likeajumprope          | 1.1
 Saskia Bollmann          | The University of Queensland       | Brisbane  | AUS     | SaskiaBollmann         | 1.1
 **- Add Entry here -**   | **- Add Entry here -**             | **Add**   | **Add** | **Add**                | 1.1
 

diff --git a/PhysIO/CHANGELOG.md b/PhysIO/CHANGELOG.md
@@ -4,10 +4,29 @@ RELEASE INFORMATION
 Current Release
 ---------------
 
-*Current version: PhysIO Toolbox Release R2022a, v8.1.0*
+*Current version: PhysIO Toolbox Release R2022b, v8.2.0*
 
-April 5th, 2022
+November 22nd, 2022
 
+Upcoming Release Notes (v8.2.0-beta)
+------------------------------------
+
+### Added
+- Interface `tapas_physio_test` to TAPAS-generic `tapas_test` function
+- Added suport for logfile version 3 of Siemens physio recordings 
+    - multi ECG/Resp channels and interleaved status messages
+    - new integration test for Siemens VB Logversion 3
+- Added support for ADInstruments/LabChart Txt-export format (see 
+  [CUBRIC Seminar Example](https://github.com/BRAIN-TO/cubric-physio) and
+  gitlab branch #107)
+
+### Fixed
+- Removed dependence on `nanmean` (Statistics Toolbox)
+    - See [GitHub issue #205](https://github.com/translationalneuromodeling/tapas/issues/205) 
+- Compatibility with multiple SPM toolbox locations for `lmod` ([GitHub issue #211](https://github.com/translationalneuromodeling/tapas/issues/211))
+    - as listed in `spm_get_defaults('tbx')`
+- Refactoring of Philips read-in to support novel 12-column logfile version, see [GitHub issue #207](https://github.com/translationalneuromodeling/tapas/issues/207#issuecomment-1246078600)
+- Unit/Integration tests for filtered traces (cardiac and respiratory) switched to absolute tolerances (relative problematic for traces close to zero)
 
 Minor Release Notes (v8.1.0)
 ----------------------------

diff --git a/PhysIO/README.md b/PhysIO/README.md
@@ -1,7 +1,7 @@
 TAPAS PhysIO Toolbox 
 ====================
 
-*Current version: Release 2022a, v8.1.0*
+*Current version: Release 2022b, v8.2.0*
 
 > Copyright (C) 2012-2022  
 > Lars Kasper  
@@ -246,7 +246,7 @@ Contributors
 ------------
 
 - Lead Programmer: 
-    - [Lars Kasper](https://www.tnu.ethz.ch/en/team/faculty-and-scientific-staff/kasper.html),
+    - [Lars Kasper](https://brain-to.ca/content/lars-kasper),
       TNU & MR-Technology Group, IBT, University of Zurich & ETH Zurich
 - Project Team: 
     - Steffen Bollmann, Centre for Advanced Imaging, University of Queensland, Australia

diff --git a/PhysIO/code/assess/tapas_physio_review.m b/PhysIO/code/assess/tapas_physio_review.m
@@ -41,8 +41,8 @@
 %
 %   See also
 
-% Author: Lars Kasper
-% Created: 2016-10-27
+% Author: Johanna Bayer, Lars Kasper
+% Created: 2016-10-27, completed 2023
 % Copyright (C) 2016 TNU, Institute for Biomedical Engineering,
 %                    University of Zurich and ETH Zurich.
 %
@@ -72,6 +72,7 @@
 sync        = scan_timing.sync;
 model       = physio.model;
 verbose     = physio.verbose;
+review      = physio.verbose.review;
 
 % Compatibility with old versions
 if ~isfield(model, 'R_column_names')
@@ -118,28 +119,126 @@
     verbose.close_figs = false;
 end
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure: Raw data
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 verbose = tapas_physio_plot_raw_physdata(ons_secs.raw, verbose);
 
-% tapas_physio_get_onsets_from_locs -> create plot function out of
-% sub-function
-% tapas_physio_get_cardiac_pulses_auto_matched -> subfunction for plot, only called
-% if in this sub-branch
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure:  Peak detection
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if ismember(preproc.cardiac.initial_cpulse_select.method, {'auto','auto_template', 'auto_matched'})
+
+    if verbose.level >=2
+        if isfield(review, 'peak')
+
+            [verbose] = tapas_physio_plot_peak_detection_from_automatically_generated(review.peak.t, review.peak.c, ...
+             review.peak.cpulse, verbose);
+        end
+    end
+end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure: Iterative template
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% First and second figure
+
+if verbose.level >= 3
+
+    if isfield(review, 'iter_temp')
+        [verbose] = tapas_physio_plot_iterative_template_creation(review.iter_temp.hasFirstGuessPeaks,...
+            review.iter_temp.t, review.iter_temp.c, review.iter_temp.cpulse1stGuess, review.iter_temp.nPulses1, ...
+            review.iter_temp.nPulses2, review.iter_temp.cpulse2ndGuess, review.iter_temp.meanLag1, ...
+            review.iter_temp.meanLag2, verbose);
+    end 
+
+% thrid figure
+    if isfield(review, 'temp_cyc')
+        [verbose] = tapas_physio_plot_templates_of_cycle_time(review.temp_cyc.tTemplate, ...
+            review.temp_cyc.template, review.temp_cyc.pulseTemplate, ... 
+            review.temp_cyc.pulseCleanedTemplate, verbose)
+    end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure:  Sync Bundles
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if verbose.level >= 3
+    if isfield(review, 'sync_bundles')
+
+        [verbose] = tapas_physio_plot_sync_bundles(review.sync_bundles.Nallvols, review.sync_bundles.t, ...
+            review.sync_bundles.SLICELOCS, verbose);
+    end
+end 
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure: Get cardiac
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if verbose.level >= 3
+
+    if isfield(review, 'get_cardiac')
+
+        [verbose] = tapas_physio_plot_get_cardiac_phase(review.get_cardiac.scannert, ...
+            review.get_cardiac.cardiac_phase, review.get_cardiac.pulset, ...
+            review.get_cardiac.svolpulse, verbose);
+    end
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure: Preproc Coutcout actual scans - all events and gradients
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 if verbose.level >= 2
     verbose.fig_handles(end+1) = ...
         tapas_physio_plot_cropped_phys_to_acqwindow(ons_secs, sqpar, verbose);
 end
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure: Preproc Respiratory filtering
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+if verbose.level>=3
+
+    if isfield(review, 'resp_filter')
+
+    [verbose] = tapas_physio_plot_filter_respiratory(review.resp_filter.rpulset, ...
+        review.resp_filter.m, review.resp_filter.s, review.resp_filter.t, ...
+        review.resp_filter.rpulset_out, review.resp_filter.rpulset_out_trend,...
+        review.resp_filter.trend,review.resp_filter.rpulset_out_trend_filt, verbose);
+
+    end 
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Figure: Preproc Diagnostics for raw physiological time series
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 [verbose, ons_secs.c_outliers_low, ons_secs.c_outliers_high, ...
     ons_secs.r_hist] = ...
     tapas_physio_plot_raw_physdata_diagnostics(ons_secs.cpulse, ...
     ons_secs.r, preproc.cardiac.posthoc_cpulse_select, verbose, ...
     ons_secs.t, ons_secs.c);
 
-% in tapas_physio_create_retroicor_regressors:
-% tapas_physio_get_respiratory_phase
-% function fh = plot_traces(pulset, rsampint, rout, resp_max, ...
-%   cumsumh, sumh, h, npulse, dpulse, rphase)
+
+if verbose.level >=3
+
+    if isfield(review, 'traces')
+        fh = tapas_physio_plot_traces(review.traces.pulset, review.traces.rsampint, ...
+            review.traces.rout, review.traces.resp_max, review.traces.cumsumh,...
+            review.traces.sumh, review.traces.h, review.traces.npulse, review.traces.dpulse, ...
+            review.traces.r_phase);
+    end 
+
+end
 
 
 %% RETROICOR
@@ -177,9 +276,25 @@
       verbose.fig_handles(end+1) = tapas_physio_plot_rvt(ons_secs, sqpar);
 end
 
-%% tapas_physio_create_hrv_regressors, tapas_physio_create_rvt_regressors
-% tapas_physio_create_noise_rois_regressors
-% => create functions out of inline-plotting
+if verbose.level >= 2
+    if model.rvt.include
+      [verbose] = tapas_physio_plot_rvt_hilbert(review.rvt_hilbert.t,review.rvt_hilbert.fr, ... 
+          review.rvt_hilbert.fr_lp, review.rvt_hilbert.fr_mag, review.rvt_hilbert.fr_rv, ... 
+    review.rvt_hilbert.fr_phase, review.rvt_hilbert.fr_if, verbose);
+    end
+end
+
+%% tapas_physio_create_hrv_regressors,
+if verbose.level>=2
+    if model.rvt.include
+        [verbose] = tapas_physio_plot_create_hrv_regressors(review.create_hrv_regressors.sample_points, ... 
+        review.create_hrv_regressors.hrOut, review.create_hrv_regressors.hr, review.create_hrv_regressors.t, ...
+        review.create_hrv_regressors.crf, review.create_hrv_regressors.convHRV, ... 
+        review.create_hrv_regressors.delays,review.create_hrv_regressors.samplePointsOut,...
+        review.create_hrv_regressors.convHRVOut, verbose);
+    end
+end
+
 
 %% Overall regressors
 

diff --git a/PhysIO/code/code b/PhysIO/code/code
diff --git a/PhysIO/code/model/tapas_physio_create_hrv_regressors.m b/PhysIO/code/model/tapas_physio_create_hrv_regressors.m
@@ -55,40 +55,16 @@
 sample_points  = tapas_physio_get_sample_points(ons_secs, sqpar, slicenum);
 hr = tapas_physio_hr(ons_secs.cpulse, sample_points);
 
-if verbose.level>=2
-    verbose.fig_handles(end+1) = tapas_physio_get_default_fig_params();
-    set(gcf, 'Name', 'Model: Regressors Heart Rate: HRV X CRF');
-    subplot(2,2,1)
-    plot(sample_points,hr,'r');xlabel('time (seconds)');
-    title('Heart Rate');
-    ylabel('beats per min (bpm)');
-end
-
-
 % Generate CRF
 dt = sqpar.TR/sqpar.Nslices;
 t = 0:dt:30;  % seconds
 crf = tapas_physio_crf(t);
 crf = crf / max(abs(crf));
 
-if verbose.level>=2
-    subplot(2,2,2)
-    plot(t, crf,'r');xlabel('time (seconds)');
-    title('Cardiac response function');
-end
-
-
 % Convolve and rescale for display purposes
 convHRV = tapas_physio_conv(hr, crf, 'causal');
 convHRV = convHRV / max(abs(convHRV));
 
-if verbose.level>=2
-    subplot(2,2,3)
-    plot(sample_points, convHRV,'r');xlabel('time (seconds)');
-    title('Heart rate X cardiac response function');
-end
-
-
 % Create shifted regressors convolved time series, which is equivalent to
 % delayed response functions according to Wikipedia (convolution)
 %
@@ -101,7 +77,7 @@
 
 % remove mean and linear trend to fulfill periodicity condition for
 % shifting
-convHRV = detrend(convHRV);
+convHRV_detrend = detrend(convHRV);
 
 % TODO: what happens at the end/beginning of shifted convolutions?
 nDelays = numel(delays);
@@ -116,7 +92,7 @@
 samplePointsOut = zeros(nScans,nSampleSlices);
 
 for iDelay = 1:nDelays
-    convHRVShifted = circshift(convHRV, nShiftSamples(iDelay));
+    convHRVShifted = circshift(convHRV_detrend, nShiftSamples(iDelay));
     for iSlice = 1:nSampleSlices
         onset_slice = sqpar.onset_slice(iSlice);
         hrOut(:,iSlice) = hr(onset_slice:sqpar.Nslices:end)';
@@ -125,14 +101,21 @@
     end
 end
 
+% save relevant structures
+verbose.review.create_hrv_regressors.sample_points = sample_points;
+verbose.review.create_hrv_regressors.hrOut = hrOut;
+verbose.review.create_hrv_regressors.hr = hr;
+verbose.review.create_hrv_regressors.t = t;
+verbose.review.create_hrv_regressors.crf = crf;
+verbose.review.create_hrv_regressors.convHRV = convHRV;
+verbose.review.create_hrv_regressors.delays = delays;
+verbose.review.create_hrv_regressors.samplePointsOut = samplePointsOut;
+verbose.review.create_hrv_regressors.convHRVOut = convHRVOut;
+
 if verbose.level>=2
-    subplot(2,2,4)
-    [tmp, iShiftMin] = min(abs(delays));
-
-    hp{1} = plot(samplePointsOut, hrOut,'k--'); hold all;
-    hp{2} = plot(samplePointsOut, squeeze(convHRVOut(:,iShiftMin,:)),'r');
-    xlabel('time (seconds)');ylabel('regessor');
-    legend([hp{1}(1), hp{2}(1)], 'heart rate (bpm)', 'cardiac response regressor');
+   [verbose] = tapas_physio_plot_create_hrv_regressors(sample_points, hrOut, ...
+    hr, t, crf, convHRV, delays,samplePointsOut, convHRVOut, verbose)
+
 end
 
 end