see CHANGELOG.md

AUTHORS.md

@@ -0,0 +1,3 @@
+**BLOCHUS** is developed by
+
+* Thomas Hiller (since 2019), [email protected]

BLOCHUS/BLOCHUS.m

@@ -33,10 +33,10 @@
 %------------- BEGIN CODE --------------
 
 %% GUI 'header' info and default GUI settings
-myui.version = '0.1.4';
-myui.date = '25.09.2020';
+myui.version = '0.1.5';
+myui.date = '30.06.2022';
 myui.author = 'Thomas Hiller';
-myui.email = 'thomas.hiller[at]leibniz-liag.de';
+myui.email = 'thomas.hiller[at]bgr.de';
 
 myui.fontsize = 9;
 myui.axfontsize = 11;

BLOCHUS/BLOCHUS_loadDefaults.m

@@ -118,7 +118,7 @@
 % pre-polarization B-field amplitude in units of [B0]
 init.PrePolFactor = [100 1e-6 1e6];
 % polar angle of pre-polarization field [deg]
-init.PrePolTheta = [90 0 360];
+init.PrePolTheta = [90 1e-3 360];
 % azimuthal angle of pre-polarization field [deg]
 init.PrePolPhi = [0 0 360];
 % pre-polarization B-field switch amplitude in units of [B0]

CHANGELOG.md

@@ -1,5 +1,16 @@
 # Changelog
 
+## [0.1.5] - 2022-06-30
+
+### Added
+- custom pre-polarization current switch-off ramps are now supported via an interpolation routine (so far only via script and in MATLAB<sup>TM</sup>)
+
+### Changed
+- now multiple angle-axis-pairs are allowed as input for function `getRotationMatrixFromAngleandAxis`
+
+### Fixed
+- fixed an issue in `getRotationMatrixFromVectors` for very small angles between vectors A and B (also edge case like parallel and anti-parallel vectors are now considered)
+
 ## [0.1.4] - 2020-09-25
 
 ### Added
@@ -43,6 +54,7 @@
 
 Initial Version
 
+[0.1.5]: https://github.com/ThoHiller/nmr-blochus/compare/v0.1.4...v0.1.5
 [0.1.4]: https://github.com/ThoHiller/nmr-blochus/compare/v0.1.3...v0.1.4
 [0.1.3]: https://github.com/ThoHiller/nmr-blochus/compare/v0.1.2...v0.1.3
 [0.1.2]: https://github.com/ThoHiller/nmr-blochus/compare/v.0.1.1...v0.1.2

README.md

@@ -48,7 +48,7 @@ In order to work properly you need to meet the following requirements:
 
 #### Operating System
 
-I tested it successfully under Windows 7 (64bit) and 10 (64bit) with Matlab R2017a and newer. Always with the latest version of the GUI Layout Toolbox (current version is v2.3.4)
+I tested it successfully under Windows 7 (64bit) and 10 (64bit) with Matlab R2017a and newer. Always with the latest version of the GUI Layout Toolbox (current version is v2.3.5)
 
 **NOTE:** So far I did not test anything on Linux or a Mac. If you get it to work on either of the two systems (which it basically should I guess) please let me know.
 
@@ -63,7 +63,7 @@ I tested it successfully under Windows 7 (64bit) and 10 (64bit) with Matlab R201
 <a name="usage"></a>
 ### Usage
 
-1. By executing the start scripts (see above)
+1. By executing the start script (see above)
 2. Simply type `BLOCHUS` on the MATLAB<sup>TM</sup> prompt (make sure the `blochus` folder is on the MATLAB<sup>TM</sup> path)
 3. Check the example scripts for the usage of the core functions without the GUI (inside the `scripts` folder)
 
@@ -87,14 +87,15 @@ In no particular order and without guarantee that it will ever happen :-) :
 ### Cite as
 If you use BLOCHUS for your research, please cite it as:
 
-Thomas Hiller. (2020, September 25). ThoHiller/nmr-blochus: v0.1.4 (Version v0.1.4). Zenodo. [https://doi.org/10.5281/zenodo.3829464]
+Thomas Hiller. (2020, September 25). ThoHiller/nmr-blochus: v0.1.5 (Version v0.1.5). Zenodo. [https://doi.org/10.5281/zenodo.3829464]
 
 Note: Even though the version number might change due to updates, this DOI is permanent (represents all versions) and always links to the latest version.
 
 
 ### References
-
-1. Hiller, T., Dlugosch, R. and Müller-Petke, M., "Utilizing pre-polarization to enhance SNMR signals - effect of imperfect switch-off", Geophysical Journal International **222**(2), p.815-826, 2020, [DOI](https://doi.org/10.1093/gji/ggaa216)
+1. Hiller, T., Costabel, S., Dlugosch, R. and Müller-Petke, M. "First Measurements of Surface Nuclear Magnetic Resonance Signals Without an Oscillating Excitation Pulse – Exploiting Non-Adiabatic Prepolarization Switch-Off", Geophysical Research Letters, **48**(23), e2021GL095371, 2021, [DOI](https://doi.org/10.1029/2021GL095371)
+1. Hiller, T., Costabel, S., Radic, T., Dlugosch, R. and Müller-Petke, M. "Feasibility study on prepolarized surface nuclear magnetic resonance for soil moisture measurements", Vadose Zone Journal, **20**(5), e20138, 2021, [DOI](https://doi.org/10.1002/vzj2.20138)
+2. Hiller, T., Dlugosch, R. and Müller-Petke, M., "Utilizing pre-polarization to enhance SNMR signals - effect of imperfect switch-off", Geophysical Journal International **222**(2), p.815-826, 2020, [DOI](https://doi.org/10.1093/gji/ggaa216)
 
 - - -
 <p style="text-align: center;"> MATLAB is a registered trademark of The Mathworks, Inc. </p>

doc/blochus/BLOCHUS/BLOCHUS.html

@@ -105,10 +105,10 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0033 <span class="comment">%------------- BEGIN CODE --------------</span>
 0034 
 0035 <span class="comment">%% GUI 'header' info and default GUI settings</span>
-0036 myui.version = <span class="string">'0.1.4'</span>;
-0037 myui.date = <span class="string">'25.09.2020'</span>;
+0036 myui.version = <span class="string">'0.1.5'</span>;
+0037 myui.date = <span class="string">'30.06.2022'</span>;
 0038 myui.author = <span class="string">'Thomas Hiller'</span>;
-0039 myui.email = <span class="string">'thomas.hiller[at]leibniz-liag.de'</span>;
+0039 myui.email = <span class="string">'thomas.hiller[at]bgr.de'</span>;
 0040 
 0041 myui.fontsize = 9;
 0042 myui.axfontsize = 11;

doc/blochus/BLOCHUS/BLOCHUS_loadDefaults.html

@@ -170,15 +170,15 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0099 init.M0 = [0 0 1];
 0100 <span class="comment">% initial magnetization [A/m]</span>
 0101 init.Minit = [1 0 0];
-0102 <span class="comment">% Earth's magnetic field [T] default: 48µT min: 1fT max: 1T</span>
+0102 <span class="comment">% Earth's magnetic field [T] default: 48µT min: 1fT max: 1T</span>
 0103 init.B0 = [48/1e6 1e-12 1];
 0104 <span class="comment">% corresponding Larmor frequencies [Hz]</span>
 0105 init.Omega0 = [<a href="../../blochus/functions/blochsim/getOmega0.html" class="code" title="function omega0 = getOmega0(gamma,B)">getOmega0</a>(init.gamma,init.B0(1))/2/pi -1e9 1e9];
-0106 <span class="comment">% T1 relaxation time [ms] default: 100ms min: 1µs max: 1000s</span>
+0106 <span class="comment">% T1 relaxation time [ms] default: 100ms min: 1µs max: 1000s</span>
 0107 init.T1relax = [100 1e-3 1e6];
-0108 <span class="comment">% T2 relaxation time [ms] default: 50ms min: 1µs max: 1000s</span>
+0108 <span class="comment">% T2 relaxation time [ms] default: 50ms min: 1µs max: 1000s</span>
 0109 init.T2relax = [50 1e-3 1e6];
-0110 <span class="comment">% simulation time [ms] default: 50ms min: 1µs max: 1000s</span>
+0110 <span class="comment">% simulation time [ms] default: 50ms min: 1µs max: 1000s</span>
 0111 init.Tsim = [50 1e-3 1e6];
 0112 
 0113 <span class="comment">% --- PRE-POLARIZATION ---</span>
@@ -189,14 +189,14 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0118 <span class="comment">% pre-polarization B-field amplitude in units of [B0]</span>
 0119 init.PrePolFactor = [100 1e-6 1e6];
 0120 <span class="comment">% polar angle of pre-polarization field [deg]</span>
-0121 init.PrePolTheta = [90 0 360];
+0121 init.PrePolTheta = [90 1e-3 360];
 0122 <span class="comment">% azimuthal angle of pre-polarization field [deg]</span>
 0123 init.PrePolPhi = [0 0 360];
 0124 <span class="comment">% pre-polarization B-field switch amplitude in units of [B0]</span>
 0125 init.PrePolSwitchFactor = [1 1e-6 1e6];
-0126 <span class="comment">% switch-off ramp time [ms] default: 1ms min: 1µs max: 1000s</span>
+0126 <span class="comment">% switch-off ramp time [ms] default: 1ms min: 1µs max: 1000s</span>
 0127 init.PrePolTramp = [1 1e-6 1e6];
-0128 <span class="comment">% switch-off ramp slope time [ms] default: 0.1ms min: 1µs max: 1000s</span>
+0128 <span class="comment">% switch-off ramp slope time [ms] default: 0.1ms min: 1µs max: 1000s</span>
 0129 init.PrePolTslope = [0.1 1e-6 1e6];
 0130 
 0131 <span class="comment">% --- PULSE ---</span>
@@ -208,7 +208,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0137 init.PulsePolarization = <span class="string">'circular'</span>;
 0138 <span class="comment">% relaxation during pulse [0/1]</span>
 0139 init.PulseRDP = 0;
-0140 <span class="comment">% pulse length [ms] default: 20ms min: 1µs max: 1000s</span>
+0140 <span class="comment">% pulse length [ms] default: 20ms min: 1µs max: 1000s</span>
 0141 init.PulseTtau = [20 1e-6 1e6];
 0142 <span class="comment">% pulse amplitude in units of [B0] default: 0.0061163 min: 1e-12 max: 1e6</span>
 0143 init.PulseB1Factor = [0.0061163 1e-12 1e6];

doc/blochus/functions/blochsim/fcn_BLOCHUS_ode.html

@@ -140,7 +140,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0057 
 0058 <span class="keyword">switch</span> param.type
 0059     <span class="keyword">case</span> <span class="string">'std'</span>
-0060         B = B0*zunit;        
+0060         B = B0*zunit;
 0061         <span class="comment">% dM/dt</span>
 0062         dM = gamma*cross(m,B) - ( (m(1)*xunit+m(2)*yunit) / T2 ) - ( ((m(3)-M0(3))*zunit) / T1 );
 0063         

doc/blochus/functions/blochsim/getMIDI_Tx.html

@@ -317,7 +317,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0246 x(locu) = I*ones(size(locu));
 0247 
 0248 <span class="comment">% now create an artificial y-component by shifting the original signal</span>
-0249 <span class="comment">% (x-component) 90° (quarter of a full period)</span>
+0249 <span class="comment">% (x-component) 90° (quarter of a full period)</span>
 0250 <span class="comment">% get the length of a quarter period</span>
 0251 t90 = dtL/4;
 0252 <span class="comment">% cut out these first samples and put them to the end of the original signal</span>
@@ -330,7 +330,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0259 <span class="comment">% pulse this is already taken care of during assembling)</span>
 0260 <span class="keyword">if</span> strcmp(param.Tx,<span class="string">'MIDI_OR'</span>) &amp;&amp; isfield(param,<span class="string">'PulseAxis'</span>)
 0261     <span class="comment">% depending on the frequency, there is a different amount of time</span>
-0262     <span class="comment">% steps for the &quot;90° phase shift&quot;</span>
+0262     <span class="comment">% steps for the &quot;90° phase shift&quot;</span>
 0263     shiftind = sum(t&lt;t90);
 0264     <span class="comment">% now shift both components by the necessary amount of samples</span>
 0265     <span class="keyword">switch</span> param.PulseAxis

doc/blochus/functions/blochsim/getPulseTimeSeries.html

@@ -214,50 +214,53 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0124         <span class="keyword">if</span> Imod.useQ &amp;&amp; Imod.Q &gt; 0
 0125             <span class="comment">% get line (band) width -&gt; f_L/Q (simple bandwidth for bandpass)</span>
 0126             Lwidth = abs(param.omega0/2/pi) / Imod.Q;
-0127             <span class="comment">% apply &quot;Breit-Wigner&quot; formula (here already normalized to 1 by</span>
-0128             <span class="comment">% multiplying with pi*Lwidth)</span>
-0129             L = 1 ./ ( ((df+Imod.Qdf).^2 ./ Lwidth.^2) + 1 );
-0130             I = I.*L;
-0131         <span class="keyword">end</span>
-0132            
-0133         <span class="comment">% get instantaneous phase due to frequency modulation</span>
-0134         theta = <a href="getPulsePhase.html" class="code" title="function theta = getPulsePhase(t,df,param,flag)">getPulsePhase</a>(t,df,param,0);
-0135         
-0136         <span class="keyword">switch</span> PulsePolarization
-0137             <span class="keyword">case</span> <span class="string">'circular'</span>
-0138                 Bout = I.*Amp.*[cos(theta + phi + phi_ax + phi_ref) <span class="keyword">...</span>
-0139                     sin(theta + phi + phi_ax + phi_ref)];
-0140             <span class="keyword">case</span> <span class="string">'linear'</span>
-0141                 Bout = 2.*I.*Amp.*[cos(theta + phi + phi_ax + phi_ref) <span class="keyword">...</span>
-0142                     0.*t];
-0143         <span class="keyword">end</span>
-0144 <span class="keyword">end</span>
-0145 <span class="comment">% if B-field values are NaN, set them to zero</span>
-0146 <span class="comment">% this can happen due to the interpolation at the end of the MIDI-pulses</span>
-0147 Bout(isnan(Bout)) = 0;
-0148 
-0149 <span class="keyword">end</span>
-0150 
-0151 <span class="comment">%------------- END OF CODE --------------</span>
-0152 
-0153 <span class="comment">%% License:</span>
-0154 <span class="comment">% GNU GPLv3</span>
-0155 <span class="comment">%</span>
-0156 <span class="comment">% BLOCHUS</span>
-0157 <span class="comment">% Copyright (C) 2019 Thomas Hiller</span>
+0127             <span class="comment">% apply Cauchy-Lorentz type formula (here already normalized to</span>
+0128             <span class="comment">% 1 by multiplying with pi*Lwidth)</span>
+0129             <span class="comment">% this is basically a Cauchy distribution PDF of the form:</span>
+0130             <span class="comment">% PDF = 1/pi * ( bw / ((f-f0)^2 + bw^2) )</span>
+0131             <span class="comment">% tweaked with some algebra</span>
+0132             L = 1 ./ ( ((df+Imod.Qdf).^2 ./ Lwidth.^2) + 1 );
+0133             I = I.*L;
+0134         <span class="keyword">end</span>
+0135            
+0136         <span class="comment">% get instantaneous phase due to frequency modulation</span>
+0137         theta = <a href="getPulsePhase.html" class="code" title="function theta = getPulsePhase(t,df,param,flag)">getPulsePhase</a>(t,df,param,0);
+0138         
+0139         <span class="keyword">switch</span> PulsePolarization
+0140             <span class="keyword">case</span> <span class="string">'circular'</span>
+0141                 Bout = I.*Amp.*[cos(theta + phi + phi_ax + phi_ref) <span class="keyword">...</span>
+0142                     sin(theta + phi + phi_ax + phi_ref)];
+0143             <span class="keyword">case</span> <span class="string">'linear'</span>
+0144                 Bout = 2.*I.*Amp.*[cos(theta + phi + phi_ax + phi_ref) <span class="keyword">...</span>
+0145                     0.*t];
+0146         <span class="keyword">end</span>
+0147 <span class="keyword">end</span>
+0148 <span class="comment">% if B-field values are NaN, set them to zero</span>
+0149 <span class="comment">% this can happen due to the interpolation at the end of the MIDI-pulses</span>
+0150 Bout(isnan(Bout)) = 0;
+0151 
+0152 <span class="keyword">end</span>
+0153 
+0154 <span class="comment">%------------- END OF CODE --------------</span>
+0155 
+0156 <span class="comment">%% License:</span>
+0157 <span class="comment">% GNU GPLv3</span>
 0158 <span class="comment">%</span>
-0159 <span class="comment">% This program is free software: you can redistribute it and/or modify</span>
-0160 <span class="comment">% it under the terms of the GNU General Public License as published by</span>
-0161 <span class="comment">% the Free Software Foundation, either version 3 of the License, or</span>
-0162 <span class="comment">% (at your option) any later version.</span>
-0163 <span class="comment">%</span>
-0164 <span class="comment">% This program is distributed in the hope that it will be useful,</span>
-0165 <span class="comment">% but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
-0166 <span class="comment">% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
-0167 <span class="comment">% GNU General Public License for more details.</span>
-0168 <span class="comment">%</span>
-0169 <span class="comment">% You should have received a copy of the GNU General Public License</span>
-0170 <span class="comment">% along with this program.  If not, see &lt;https://www.gnu.org/licenses/&gt;.</span></pre></div>
+0159 <span class="comment">% BLOCHUS</span>
+0160 <span class="comment">% Copyright (C) 2019 Thomas Hiller</span>
+0161 <span class="comment">%</span>
+0162 <span class="comment">% This program is free software: you can redistribute it and/or modify</span>
+0163 <span class="comment">% it under the terms of the GNU General Public License as published by</span>
+0164 <span class="comment">% the Free Software Foundation, either version 3 of the License, or</span>
+0165 <span class="comment">% (at your option) any later version.</span>
+0166 <span class="comment">%</span>
+0167 <span class="comment">% This program is distributed in the hope that it will be useful,</span>
+0168 <span class="comment">% but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+0169 <span class="comment">% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+0170 <span class="comment">% GNU General Public License for more details.</span>
+0171 <span class="comment">%</span>
+0172 <span class="comment">% You should have received a copy of the GNU General Public License</span>
+0173 <span class="comment">% along with this program.  If not, see &lt;https://www.gnu.org/licenses/&gt;.</span></pre></div>
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