Merge pull request #24 from likeajumprope/development

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.

Contributor-License-Agreement.md

@@ -22,6 +22,7 @@ Niklas Bürgi             | SNS, University of Zurich          | Zurich    | CH
 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
 
 (hereinafter referred to as "Contributor")

PhysIO/CHANGELOG.md

@@ -4,19 +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 and 
+    - 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)
 ----------------------------

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

PhysIO/code/readin/tapas_physio_read_columnar_textfiles.m

@@ -2,11 +2,11 @@
 % Reads _PULS, _RESP, _ECG, _Info-files from Siemens tics format with
 % multiple numbers of columns and different column headers
 %
-%   output = tapas_physio_read_columnar_textfiles(input)
+%   [C, columnNames] = tapas_physio_read_columnar_textfiles(fileName, fileType)
 %
 % IN
 %   fileName    *.log from Siemens VD/VE tics file format
-%   fileType    'ECG', 'PULS', 'RESP', 'Info', 'BIOPAC_TXT'
+%   fileType    'ECG', 'PULS', 'RESP', 'Info', 'BIOPAC_TXT', 'PHILIPS'
 %               If not specified, this is read from the last part of the
 %               filename after the last underscore, e.g.
 %               Physio_*_ECG.log -> log
@@ -56,6 +56,16 @@
 
 
 switch upper(fileType)
+    case {'ADINSTRUMENTS_TXT', 'LABCHART_TXT'}
+        strColumnHeader = 'ChannelTitle=';
+
+        %sub-02 from CUBRIC
+        parsePatternPerNColumns{4} = '%f %f %f %f';
+        nEmptyLinesAfterHeader(4) = 1;
+
+        %sub-01 from CUBRIC
+        parsePatternPerNColumns{7} = '%f %f %f %f %f %f %f';
+        nEmptyLinesAfterHeader(7) = 4;
     case 'BIDS'
         strColumnHeader = '';
         parsePatternPerNColumns{3} = '%f %f %f';
@@ -80,6 +90,14 @@
         nEmptyLinesAfterHeader(3) = 0;
         nEmptyLinesAfterHeader(4) = 1;
         nEmptyLinesAfterHeader(5) = 1;
+    case 'PHILIPS'
+        strColumnHeader = 'v1raw'; % Philips header similar to: # v1raw v2raw  v1 v2  ppu resp vsc  gx gy gz mark mark2
+        parsePatternPerNColumns{10} = '%d %d %d %d %d %d %d %d %d %s';
+        parsePatternPerNColumns{11} = '%d %d %d %d %d %d %d %d %d %s %s'; % log file version 2 with two marker columns
+        parsePatternPerNColumns{12} = '%d %d %d %d %d %d %d %d %d %d %s %s'; %  logfile version 3(?, from Nottingham) with 'vsc' column
+        nEmptyLinesAfterHeader(10) = 0;
+        nEmptyLinesAfterHeader(11) = 0;
+        nEmptyLinesAfterHeader(12) = 0;        
     case {'PULS', 'RESP', 'ECG'} % have similar format
         % Cologne (RESP/PULS/ECG for 2nd column):
         %   Time_tics RESP Signal
@@ -104,20 +122,27 @@
 while ~haveFoundColumnHeader
     nHeaderLines = nHeaderLines + 1;
     strLine = fgets(fid);
-    haveFoundColumnHeader = any(regexp(upper(strLine), strColumnHeader));
+    haveFoundColumnHeader = any(regexpi(strLine, strColumnHeader));
 end
 
 switch upper(fileType)
+    case {'ADINSTRUMENTS_TXT', 'LABCHART_TXT'}
+        columnNames = regexp(strLine, '([\t])', 'split');
+        nColumns = numel(columnNames);
     case 'BIDS' % will be in separate json-file
         columnNames = {};
         nColumns = 3;
     case 'BIOPAC_TXT' % bad column names with spaces...e.g. 'RESP - RSP100C'
         columnNames = regexp(strLine, '([\t])', 'split');
         nColumns = numel(columnNames);
+    case 'PHILIPS'
+        columnNames = regexp(strLine, '([\w]*)', 'tokens');
+        columnNames = [columnNames{:}]; % cell of cell into cell of strings
+        nColumns = numel(columnNames);
     otherwise
         columnNames = regexp(strLine, '([\w]*)', 'tokens');
         columnNames = [columnNames{:}]; % cell of cell into cell of strings
-        nColumns = numel(regexp(strLine, ' *')) + 1; % columns are separated by arbitrary number of spaces
+        nColumns = numel(regexp(strLine, ' *')) + 1; % columns are separated by arbitrary number of spaces...TODO: Why + 1?
 end
 fclose(fid);
 
@@ -126,8 +151,10 @@
 % now read the rest of the file
 fid = fopen(fileName);
 switch upper(fileType)
-    case {'BIDS', 'BIOPAC_TXT', 'INFO', 'PULS', 'RESP'}
+    case {'ADINSTRUMENTS_TXT', 'LABCHART_TXT', 'BIDS', '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', '#');
     case {'ECG'}
         C = textscan(fid, parsePatternPerNColumns{nColumns}, 'HeaderLines', nHeaderLines);
         if nColumns == 4 % CMRR, different ECG channels possible!

PhysIO/code/readin/tapas_physio_read_physlogfiles.m

@@ -59,6 +59,9 @@
 end
 
 switch lower(log_files.vendor)
+    case {'adinstruments_txt', 'labchart_txt'}
+        [c, r, t, cpulse, acq_codes] = ...
+            tapas_physio_read_physlogfiles_adinstruments_txt(log_files, cardiac_modality, verbose);
     case 'bids'
         [c, r, t, cpulse, acq_codes] = ...
             tapas_physio_read_physlogfiles_bids(log_files, cardiac_modality, verbose);