jemris version number 2.9.2

JEMRIS · Jan 3, 2025 · 3a4eeae · 3a4eeae
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@ cmake_minimum_required (VERSION 2.8)
 project (jemris) 
 set (jemris_VERSION_MAJOR 2)
 set (jemris_VERSION_MINOR 9)
-set (jemris_VERSION_PATCH 1)
+set (jemris_VERSION_PATCH 2)
 set (jemris_VERSION "${jemris_VERSION_MAJOR}.${jemris_VERSION_MINOR}.${jemris_VERSION_PATCH}")
 
 set(CMAKE_BUILD_TYPE "Release")

diff --git a/debian/changelog b/debian/changelog
@@ -1,12 +1,19 @@
+jemris (2.9-2) stable; urgency=low
+  * Major support of sundials library 6.4 (no backward compatibility with older versions)
+  * Minor improved test metrics for unit tests (sanityck)
+  * Minor bug fixes
+  * Minor updated documentation
+
+ -- Tony Stoecker <tony.stoecker@dzne.de>  Fr, 03 Jan 2025 11:56:45 +0200
 
- -- Tony Stoecker <tony.stoecker@dzne.de>  Thu, 08 Sep 2023 11:56:45 +0200
 jemris (2.9-1) stable; urgency=low
   * Major support of sundials cvode library 5.8 (no backward compatibility with older versions < 5.x)
   * Major added linux matlab standalone GUIs (such that MATLAB is not needed for using the GUIs)
   * Minor bug fixes
   * Minor updated documentation
 
- -- Tony Stoecker <tony.stoecker@dzne.de>  Thu, 03 Feb 2022 11:56:45 +0200
+ -- Tony Stoecker <tony.stoecker@dzne.de>  Thu, 08 Sep 2023 11:56:45 +0200
+
 jemris (2.9-0) stable; urgency=low
   * Major added image reconstruction and ismrmrd support
   * Major added deformable motion simulation

diff --git a/doc/doxy.conf b/doc/doxy.conf
@@ -32,7 +32,7 @@ PROJECT_NAME           = jemris
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 2.9.1
+PROJECT_NUMBER         = 2.9.2
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer

diff --git a/doc/userguide/ug_main.dox b/doc/userguide/ug_main.dox
@@ -189,8 +189,8 @@ Finally, a c++ framework extension is shown.
  \page ug_about About JEMRIS
 \section ug_version Version
 
-JEMRIS Version 2.9.1\n
-Copyright (C) 2006-2023  Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder \n
+JEMRIS Version 2.9.2\n
+Copyright (C) 2006-2025  Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder \n
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -240,10 +240,9 @@ Some projects extended JEMRIS and added new functionality to the software. Here
 Marten Veldmann implemented the <b> ISMRMRD data format </b> into JEMRIS. With this feature, the simulation data can be feeded into image reconstuction 
 software which is compatible with ISMRMRD. Marten also implemented a fully <b> automated image reconstruction pipeline </b> as a Docker service
 for JEMRIS. The pipeline is installed during JEMRIS installation (see \ref ug_install). Furthermore, Marten updated and extended the Pulseq support 
-of JEMRIS (see below) to the newest Pulseq version. The reconstruction pipeline is compatible with JEMRIS simulations and real MR data acquired with
-Pulseq sequences. More information on the pipeline can be found on <a href=" https://github.com/mrphysics-bonn/python-ismrmrd-reco"><b>github</b></a>.
-The complete process - sequence development, acquisition, and image reconstuction - was presented at the ISMRM 2021 conference:
-<i>	Open-Source MR Imaging Workflow. Veldmann M, Ehses P, Chow K, Zaitsev M, Stöcker T, ISMRM 2021, #0729</i>
+of JEMRIS (see below) to the newest Pulseq version. Please read this paper for more information: <a href=" https://github.com/mrphysics-bonn/python-ismrmrd-reco"><b>github</b></a>.
+and in this paper:
+<i>Veldmann, Marten, Philipp Ehses, Kelvin Chow, Jon‐Fredrik Nielsen, Maxim Zaitsev, and Tony Stöcker. “Open‐source MR Imaging and Reconstruction Workflow.” Magnetic Resonance in Medicine 88, no. 6 (December 2022): 2395–2407.</i> <a>https://doi.org/10.1002/mrm.29384</a>
 
 <b> 2021b</b>\n 
 2021: Ben Hoshino and Xin Chen from Canon Medical Research significantly improved JEMRIS simulation performance (since version 2.9.0).
@@ -252,7 +251,7 @@ This results in up to 3x faster simulations! (Depending on the complexity of the
 
 <b> 2021a</b>\n 
 Hanna Hanson and Benny Rowland implemented <b> motion of deformable phantoms </b> into JEMRIS, which can e.g. be used for realistic simulations of cardiac MRI or respiration.
-An example can be found on  <a href=" https://github.com/hmhanson/4DPhantomMRI"><b>Hanna's github page</b></a>. Read this paper for more information:
+An example can be found on  <a href=" https://github.com/hmhanson/4DPhantomMRI"><b>Hanna's github page</b></a>. Please read this paper for more information:
 <i> Hanson, H.M. , Eiben, B.,  McClelland, J.R., van Herk, M. & Rowland, B.C. (2021) 4D Deformable Digital Phantom for MRI %Sequence Development. Medical Physics. </i>
 <a>https://aapm.onlinelibrary.wiley.com/doi/10.1002/mp.15036</a>
 \n\n

diff --git a/share/examples/approved/epi.seq b/share/examples/approved/epi.seq
@@ -1,5 +1,5 @@
 # Pulseq sequence format
-# Created by JEMRIS 2.9.1
+# Created by JEMRIS 2.9.2
 
 [VERSION]
 major 1
@@ -195,4 +195,4 @@ num_samples 100
 
 [SIGNATURE]
 Type md5
-Hash 1e7d4cf7131501b13ffcd835f6956485
+Hash ef263f03f4babe80d6c51b7d9bb25c86
diff --git a/share/examples/approved/gre.seq b/share/examples/approved/gre.seq
@@ -1,5 +1,5 @@
 # Pulseq sequence format
-# Created by JEMRIS 2.9.1
+# Created by JEMRIS 2.9.2
 
 [VERSION]
 major 1
@@ -301,4 +301,4 @@ num_samples 100
 
 [SIGNATURE]
 Type md5
-Hash d68b31c6e784812dc126f1b2ed885506
+Hash 38a7acf6b7fe7c9960fe3db99bf3bcbb
diff --git a/share/examples/approved/radial.seq b/share/examples/approved/radial.seq
@@ -1,5 +1,5 @@
 # Pulseq sequence format
-# Created by JEMRIS 2.9.1
+# Created by JEMRIS 2.9.2
 
 [VERSION]
 major 1
@@ -333,4 +333,4 @@ num_samples 958
 
 [SIGNATURE]
 Type md5
-Hash 4f0f2a91fec4681991b510a403e3268e
+Hash 15d1a36e3028c40aebede740cf2f184b
diff --git a/share/examples/approved/sli_sel.seq b/share/examples/approved/sli_sel.seq
@@ -1,5 +1,5 @@
 # Pulseq sequence format
-# Created by JEMRIS 2.9.1
+# Created by JEMRIS 2.9.2
 
 [VERSION]
 major 1
@@ -937,4 +937,4 @@ num_samples 2667
 
 [SIGNATURE]
 Type md5
-Hash c874704b8f21835afb78780fcffda7ea
+Hash c25ab20c2444bec997d34d8bacb93edb
diff --git a/share/examples/approved/trapezoid.seq b/share/examples/approved/trapezoid.seq
@@ -1,5 +1,5 @@
 # Pulseq sequence format
-# Created by JEMRIS 2.9.1
+# Created by JEMRIS 2.9.2
 
 [VERSION]
 major 1
@@ -56,4 +56,4 @@ num_samples 100
 
 [SIGNATURE]
 Type md5
-Hash 8e2ec63af9701af635a21c1efe6d2a4e
+Hash 54568a146eb11adc8f018a447d5b5e26
diff --git a/share/matlab/Contents.m b/share/matlab/Contents.m
@@ -32,7 +32,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/JEMRIS_ContainerSequence.m.in b/share/matlab/JEMRIS_ContainerSequence.m.in
@@ -3,7 +3,7 @@ function varargout = JEMRIS_ContainerSequence(varargin)
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/JEMRIS_seq.m.in b/share/matlab/JEMRIS_seq.m.in
@@ -3,7 +3,7 @@ function varargout = JEMRIS_seq(varargin)
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/JEMRIS_sim.m.in b/share/matlab/JEMRIS_sim.m.in
@@ -3,7 +3,7 @@ function varargout = JEMRIS_sim (varargin)
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/JEMRIS_txrx.m.in b/share/matlab/JEMRIS_txrx.m.in
@@ -3,7 +3,7 @@ function varargout = JEMRIS_txrx(varargin)
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/brainSample.m b/share/matlab/brainSample.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/calcBfromXi.m b/share/matlab/calcBfromXi.m
@@ -18,7 +18,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/changeSeqAttributes.m b/share/matlab/changeSeqAttributes.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/changeSeqTree.m b/share/matlab/changeSeqTree.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/getAllModules.m b/share/matlab/getAllModules.m
@@ -6,7 +6,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/parseXMLseq.m b/share/matlab/parseXMLseq.m
@@ -4,7 +4,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/plotCoils.m b/share/matlab/plotCoils.m
@@ -4,7 +4,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/plotSeqTree.m b/share/matlab/plotSeqTree.m
@@ -4,7 +4,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/plotsensitivity.m b/share/matlab/plotsensitivity.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/plotseq.m b/share/matlab/plotseq.m
@@ -6,7 +6,7 @@
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/plotsim.m b/share/matlab/plotsim.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/readEvol.m b/share/matlab/readEvol.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/seqcad_uitoolbar.m b/share/matlab/seqcad_uitoolbar.m
@@ -5,7 +5,7 @@
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/matlab/writeSample.m b/share/matlab/writeSample.m
@@ -26,7 +26,7 @@
 
 %
 %  JEMRIS Copyright (C)
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %

diff --git a/share/matlab/writeXMLseq.m b/share/matlab/writeXMLseq.m
@@ -6,7 +6,7 @@ function writeXMLseq(handles,S,dnode,docNode)
 
 %
 %  JEMRIS Copyright (C) 
-%                        2006-2023  Tony Stoecker
+%                        2006-2025  Tony Stoecker
 %                        2007-2015  Kaveh Vahedipour
 %                        2009-2019  Daniel Pflugfelder
 %                                  

diff --git a/share/python/jemris.py b/share/python/jemris.py
@@ -1,6 +1,6 @@
 """
 JEMRIS Copyright (C)
-                      2006-2023  Tony Stoecker
+                      2006-2025  Tony Stoecker
                       2007-2019  Kaveh Vahedipour
                       2009-2019  Daniel Pflugfelder
                       2018-2019  Markus Zimmermann

diff --git a/src/AnalyticCoil.cpp b/src/AnalyticCoil.cpp
@@ -7,7 +7,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *                                  

diff --git a/src/AnalyticCoil.h b/src/AnalyticCoil.h
@@ -7,7 +7,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *                                  

diff --git a/src/AnalyticGradPulse.cpp b/src/AnalyticGradPulse.cpp
@@ -4,7 +4,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *                                  

diff --git a/src/AnalyticGradPulse.h b/src/AnalyticGradPulse.h
@@ -4,7 +4,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *                                  

diff --git a/src/AnalyticPulseShape.cpp b/src/AnalyticPulseShape.cpp
@@ -4,7 +4,7 @@
 
 /*
  *  JEMRIS Copyright (C)
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *

diff --git a/src/AnalyticPulseShape.h b/src/AnalyticPulseShape.h
@@ -4,7 +4,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *                                  

diff --git a/src/AnalyticRFPulse.cpp b/src/AnalyticRFPulse.cpp
@@ -4,7 +4,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *                                  

diff --git a/src/AnalyticRFPulse.h b/src/AnalyticRFPulse.h
@@ -4,7 +4,7 @@
 
 /*
  *  JEMRIS Copyright (C) 
- *                        2006-2023  Tony Stoecker
+ *                        2006-2025  Tony Stoecker
  *                        2007-2018  Kaveh Vahedipour
  *                        2009-2019  Daniel Pflugfelder
  *