codespell: add config and action to codespell the code to avoid known typos, fix typos

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+# some abbreviated citations etc
+ignore-regex = .*Reson\. Ser.*
+ignore-words-list = te,fo,nd,maked,datas,iten,itel,tread

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

doc/doxy.conf.in

@@ -916,7 +916,7 @@ HTML_STYLESHEET        =
 # user-defined cascading style sheet that is included after the standard
 # style sheets created by doxygen. Using this option one can overrule
 # certain style aspects. This is preferred over using HTML_STYLESHEET
-# since it does not replace the standard style sheet and is therefor more
+# since it does not replace the standard style sheet and is therefore more
 # robust against future updates. Doxygen will copy the style sheet file to
 # the output directory.
 
@@ -1679,7 +1679,7 @@ UML_LOOK               = NO
 # the class node. If there are many fields or methods and many nodes the
 # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
 # threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
+# manageable. Set this to 0 for no limit. Note that the threshold may be
 # exceeded by 50% before the limit is enforced.
 
 UML_LIMIT_NUM_FIELDS   = 10

doc/seqcode.sty

@@ -2,7 +2,7 @@
 %%   This is file `seqcode.sty'
 %%
 %%   It is supposed to help you easily include MATLAB source code
-%%   into LaTeX document, but have it nicely highlighted, unsing
+%%   into LaTeX document, but have it nicely highlighted, using
 %%   the great listings package.
 %%
 %%   Usage: Include your MATLAB source code by using
@@ -136,7 +136,7 @@
     linewidth={\textwidth}
 }
 
-\ifbw % use font formating and gray 'colors'
+\ifbw % use font formatting and gray 'colors'
     \newcommand\keywordcolor{\bfseries}
 	\lstset{language=matlabfloz,							% use our version of highlighting
 		keywordstyle=\bfseries, 							% keywords in bold

matlab/+mr/@Sequence/Sequence.m

@@ -48,7 +48,7 @@
         rfLibrary;        % Library of RF events
         gradLibrary;      % Library of gradient events
         adcLibrary;       % Library of ADC readouts
-        trigLibrary;      % Library of trigger events ( referenced from the extentions library )
+        trigLibrary;      % Library of trigger events ( referenced from the extensions library )
         labelsetLibrary;  % Library of Label(set) events ( reference from the extensions library )
         labelincLibrary;  % Library of Label(inc) events ( reference from the extensions library )
         extensionLibrary; % Library of extension events. Extension events form single-linked zero-terminated lists
@@ -270,7 +270,7 @@ function setDefinition(seqObj,key,val)
         function addBlock(obj,varargin)
             %addBlock Add a new block to the sequence.
             %   addBlock(obj, blockStruct) Adds a sequence block with
-            %   provided as a block struture
+            %   provided as a block structure
             %
             %   addBlock(obj, e1, e2, ...) Adds a block with multiple
             %   events e1, e2, etc.
@@ -297,7 +297,7 @@ function modGradAxis(obj,axis,modifier)
             allGradEvents = paren2(vertcat(obj.blockEvents{:}),3:5);
 
             selectedEvents=unique(allGradEvents(:,channelNum));
-            selectedEvents=selectedEvents(0~=selectedEvents); % elliminate 0
+            selectedEvents=selectedEvents(0~=selectedEvents); % eliminate 0
             otherEvents=unique(allGradEvents(:,otherChans));
             assert(isempty(intersect(selectedEvents,otherEvents)),'ERROR: the same gradient event is used on multiple axes, this is not yet supported by modGradAxis()');
 
@@ -397,7 +397,7 @@ function flipGradAxis(obj, axis)
 
         function [id shapeIDs]=registerRfEvent(obj, event)
             % registerRfEvent Add the event to the libraries (object,
-            % shapes, etc and retur the event's ID. This I can be stored in
+            % shapes, etc and return the event's ID. This I can be stored in
             % the object to accelerate addBlock()
 
             mag = abs(event.signal);
@@ -671,7 +671,7 @@ function setBlock(obj, index, varargin)
                 % key mapping then... The trick is that we rely on the
                 % sorting of the extension IDs and then we can always find
                 % the last one in the list by setting the reference to the
-                % next to 0 and then proceed with the otehr elements.
+                % next to 0 and then proceed with the other elements.
                 [~,I]=sort([extensions(:).ref]);
                 extensions=extensions(I);
                 all_found=true;
@@ -729,7 +729,7 @@ function setBlock(obj, index, varargin)
                                 end
                             end
                         else
-                            error('Error in block %d: Gradient starting at non-zero value need to be preceded by a comptible gradient', index);
+                            error('Error in block %d: Gradient starting at non-zero value need to be preceded by a compatible gradient', index);
                         end
                     else                   
                         error('First gradient in the the first block has to start at 0.');
@@ -951,7 +951,7 @@ function setBlock(obj, index, varargin)
             c_excitation=0;
             c_refocusing=0;
             c_adcSamples=0;
-            % loop throught the blocks to prepare preallocations
+            % loop through the blocks to prepare preallocations
             for iB=1:length(obj.blockEvents)
                 block = obj.getBlock(iB);
                 if ~isempty(block.rf)
@@ -1024,7 +1024,7 @@ function setBlock(obj, index, varargin)
 %                     ii_next_refocusing = min(length(i_refocusing),ii_next_refocusing+1);
 %                 end
 %             end
-            i_periods=sort([1; i_excitation+1; i_refocusing+1; size(gw,2)+1]); % we need thise +1 for compatibility with the above code which prooved to be correct
+            i_periods=sort([1; i_excitation+1; i_refocusing+1; size(gw,2)+1]); % we need these +1 for compatibility with the above code which proved to be correct
             ii_next_excitation=min(length(i_excitation),1);
             ii_next_refocusing=min(length(i_refocusing),1);
             ktraj=zeros(size(gw));
@@ -1163,7 +1163,7 @@ function setBlock(obj, index, varargin)
                 block = obj.getBlock(iB);
                 isValid = t0+obj.blockDurations(iB)>timeRange(1) && t0<=timeRange(2);
                 if isValid
-                    if isfield(block,'label') %current labels, works on the curent or next adc
+                    if isfield(block,'label') %current labels, works on the current or next adc
                         for i=1:length(block.label)
                             if strcmp(block.label(i).type,'labelinc')
                                 label_store.(block.label(i).label)=...
@@ -1248,7 +1248,7 @@ function setBlock(obj, index, varargin)
             setAxesZoomMotion(h,ax(1),'horizontal');
         end
 
-        function grad_waveforms=gradient_waveforms1(obj) % currently disfunctional (feature_ExtTrap)
+        function grad_waveforms=gradient_waveforms1(obj) % currently dysfunctional (feature_ExtTrap)
             % gradient_waveforms()
             %   Decompress the entire gradient waveform
             %   Returns an array of gradient_axes x timepoints
@@ -1633,7 +1633,7 @@ function setBlock(obj, index, varargin)
                 end
                 gm_pp{i}=fnint(gw_pp{i});
                 tc{end+1}=gm_pp{i}.breaks;
-                % "sample" ramps for display purposes otherwise piecewise-linear diplay (plot) fails (looks stupid)
+                % "sample" ramps for display purposes otherwise piecewise-linear display (plot) fails (looks stupid)
                 ii=find(abs(gm_pp{i}.coefs(:,1))>eps);
                 if ~isempty(ii)
                     tca=cell(1,length(ii));
@@ -1660,7 +1660,7 @@ function setBlock(obj, index, varargin)
             tacc=1e-10; % temporal accuracy
             taccinv=1/tacc;
             t_ktraj = tacc*unique(round(taccinv*[tc{:}, 0, t_excitation-2*obj.rfRasterTime, t_excitation-obj.rfRasterTime, t_excitation, t_refocusing-obj.rfRasterTime, t_refocusing, t_adc, total_duration]));
-            % % the "proper" matlab's function ismember() is slow and returns a bool array, but builtin('_ismemberhelper'...) is not compatible accross versions (known not to work on the windows 2021a version)
+            % % the "proper" matlab's function ismember() is slow and returns a bool array, but builtin('_ismemberhelper'...) is not compatible across versions (known not to work on the windows 2021a version)
             %[~,i_excitation]=builtin('_ismemberhelper',tacc*round(taccinv*t_excitation),t_ktraj);
             %[~,i_refocusing]=builtin('_ismemberhelper',tacc*round(taccinv*t_refocusing),t_ktraj);
             %[~,i_adc]=builtin('_ismemberhelper',tacc*round(taccinv*t_adc),t_ktraj);
@@ -1754,7 +1754,7 @@ function setBlock(obj, index, varargin)
             % filter like we did it in the gradient music project
             %b = fir1(40, 10000/sample_rate);
             %sound_data = filter(b, 1, sound_data,[],2);
-            % use Gaussian convolution instead to supress ringing
+            % use Gaussian convolution instead to suppress ringing
             gw=gausswin(round(sample_rate/6000)*2+1);
             gw=gw/sum(gw(:));
             sound_data(1,:) = conv(sound_data(1,:), gw, 'same');
@@ -1863,7 +1863,7 @@ function setBlock(obj, index, varargin)
         end
 
         function id = getExtensionTypeID(obj, str) 
-            % get numeric ID for the given string extention ID
+            % get numeric ID for the given string extension ID
             % will automatically create a new ID if unknown 
             num=find(strcmp(obj.extensionStringIDs,str));
             if isempty(num)
@@ -1881,7 +1881,7 @@ function setBlock(obj, index, varargin)
         end
 
         function str = getExtensionTypeString(obj, id)
-            % get numeric ID for the given string extention ID
+            % get numeric ID for the given string extension ID
             % may fail 
             num=find(obj.extensionNumericIDs==id);
             if isempty(num)
@@ -1891,7 +1891,7 @@ function setBlock(obj, index, varargin)
         end
 
         function setExtensionStringAndID(obj, str, id) 
-            % set numeric ID for the given string extention ID
+            % set numeric ID for the given string extension ID
             % may fail if not unique
             if any(strcmp(obj.extensionStringIDs,str)) || any(obj.extensionNumericIDs==id) 
                 error('Numeric or String ID is not unique');

matlab/+mr/@Sequence/read.m

@@ -192,7 +192,7 @@ function read(obj,filename,varargin)
 
     % for versions prior to 1.4.0 blockDurations have not been initialized
     obj.blockDurations=zeros(1,length(obj.blockEvents));
-    % scan trhough blocks and calculate durations
+    % scan through blocks and calculate durations
     for iB = 1:length(obj.blockEvents)
         b=obj.getBlock(iB);
         if delayInd_tmp(iB) > 0
@@ -497,7 +497,7 @@ function read(obj,filename,varargin)
 
     function nextLine = skipComments(fid, stopBeforeSection)
         %skipComments Read lines of skipping blank lines and comments.
-        %   line=skipComments(fid) Read lines from valid file identifer and
+        %   line=skipComments(fid) Read lines from valid file identifier and
         %   return the next non-comment line.
 
         if (nargin<2)

matlab/+mr/addGradients.m

@@ -2,7 +2,7 @@
 %addGradients Superposition of several gradients
 %
 %   [grad] = addGradients(grads, system) 
-%   Returns the superposition of serveral gradients
+%   Returns the superposition of several gradients
 %   gradients have to be passed as a cell array e.g. {g1, g2, g3}
 %
 %   See also  Sequence.addBlock  mr.opts  makeTrapezoid
@@ -114,7 +114,7 @@
     for ii = 1:length(grads)
         g=grads{ii};
         if strcmp(g.type,'trap')
-            if g.flatTime>0 % trapezoid or triange
+            if g.flatTime>0 % trapezoid or triangle
                 g.tt=cumsum([0 g.riseTime g.flatTime g.fallTime]);
                 g.waveform=[0 g.amplitude g.amplitude 0];
             else

matlab/+mr/calcDuration.m

@@ -32,7 +32,7 @@
 %                 % containing one sample will be zero
 %                 % however, we do not have access to the gradient raster time
 %                 % here, so we opt of a hack, but it will actually fail for the
-%                 % gradint containg one sample...
+%                 % gradint containing one sample...
 %                 % event.t(2) - event.t(1) gives us one gradient raster time
 %                 duration=max(duration, event.t(end) + event.t(2) - event.t(1) + event.delay ); 
                 duration=max(duration, event.delay+event.shape_dur); % shaped gradient has now a field called 'shape_dur' because it is impossible to calculate duration here in a general case...

matlab/+mr/calcRamp.m

@@ -141,7 +141,7 @@
 %
 %  1. Calculate optimal k-space point kopt that would lie on a straight 
 %     line of N=UsePoints evenly spaced points to kend. If this kopt can be 
-%     reached within gradient and slew limts, kopt is the solution of this
+%     reached within gradient and slew limits, kopt is the solution of this
 %     function call. 
 %
 %  2. If kopt cannot be reached, calculate the gradient limited point kgl 

matlab/+mr/calcRfBandwidth.m

@@ -21,7 +21,7 @@
 
 tc=mr.calcRfCenter(rf);
 
-% resample the pulse to a resonable time array
+% resample the pulse to a reasonable time array
 nn=round(1/df/dt);
 t=(-floor(nn/2):ceil(nn/2)-1)*dt;
 

matlab/+mr/checkTiming.m

@@ -20,7 +20,7 @@
         if isnumeric(e) % special handling for blockDuration
             continue;
         end
-        assert(isstruct(e), 'wrong format of the variable aguments, list of structures is expected');
+        assert(isstruct(e), 'wrong format of the variable arguments, list of structures is expected');
         ok=true;
         if length(e)>1
             % for now this is only the case for arrays of extensions, but

matlab/+mr/compile_mex.m

@@ -4,7 +4,7 @@
 %
 % The Pulseq toolbox has been designed such that these files are *not*
 % necessary to use the toolbox, but if they are present a substantial
-% performance improvement can be acheived.
+% performance improvement can be achieved.
 %
 % The script relies on the MATLAB Coder package, available in later
 % versions of MATLAB.

matlab/+mr/convert.m

@@ -1,7 +1,7 @@
 function out=convert(in,varargin)
 %OPTS Set gradient limits of the MR system.
 %   out=convert(in,from,to) Convert the numerical data in, given in
-%   specificed units 'from' to units specified in 'to'.
+%   specified units 'from' to units specified in 'to'.
 %
 %   Valid unit strings are:
 %    'Hz/m' 'mT/m' 'rad/ms/mm' 'Hz/m/s' 'mT/m/ms' 'T/m/s' 'rad/ms/mm/ms'

matlab/+mr/getSupportedLabels.m

@@ -1,5 +1,5 @@
 function supported_labels = getSupportedLabels()
-% auxilary function
+% auxiliary function
 
 supported_labels={'SLC','SEG','REP','AVG','SET','ECO','PHS','LIN','PAR','NAV','REV','SMS', ... # these label values are copied to the corresponding MDH field on Siemens
         'PMC', ... # for MoCo/PMC Pulseq version to recognize blocks that can be prospectively corrected for motion 

matlab/+mr/getSupportedRfUse.m

@@ -1,5 +1,5 @@
 function supported_rf_use = getSupportedRfUse()
-% auxilary function
+% auxiliary function
 
 supported_rf_use={'excitation','refocusing','inversion','saturation','preparation'};
 

matlab/+mr/makeAdiabaticPulse.m

@@ -164,7 +164,7 @@
 pm=cumsum(fm)*opt.dwell;
 
 [dfm,ifm]=min(abs(fm)); % find the center of the pulse
-% we will also use the ocasion to find the rate of change of the frequency
+% we will also use the occasion to find the rate of change of the frequency
 % at the center of the pulse
 if dfm==0 
     pm0=pm(ifm);

matlab/+mr/makeArbitraryRf.m

@@ -1,6 +1,6 @@
 function [rf, gz, gzr, delay] = makeArbitraryRf(signal,flip,varargin)
 %makeArbitraryRf Create an RF pulse with the given pulse shape.
-%   rf=makeArbitraryRf(singal, flip) Create RF pulse with complex signal 
+%   rf=makeArbitraryRf(signal, flip) Create RF pulse with complex signal 
 %   and given flip angle (in radians)
 %
 %   rf=makeArbitraryRf(..., 'FreqOffset', f,'PhaseOffset',p)

matlab/+mr/makeExtendedTrapezoidArea.m

@@ -28,7 +28,7 @@
     Gp=sys.maxGrad*sign(Gp);
     obj2=@(x) (A-testGA(Gp,x,SR,sys.gradRasterTime,Gs,Ge)).^2;
     [T,obj2val,exitf] = fminsearch(obj2,0);
-    assert(obj2val<1e-2); % did the final search converge? MZ: I had to reduce the theshold...
+    assert(obj2val<1e-2); % did the final search converge? MZ: I had to reduce the threshold...
 
     Tp=ceil(T/sys.gradRasterTime)*sys.gradRasterTime;
 

matlab/+mr/makeGaussPulse.m

@@ -10,10 +10,10 @@
 %   slice select gradient corresponding to given slice thickness (m).
 %
 %   [rf, gz]=makeGaussPulse(flip,lims,...) Create slice selection gradient 
-%   with the specificed gradient limits (e.g. amplitude, slew).
+%   with the specified gradient limits (e.g. amplitude, slew).
 %
 %   [rf, gz, gzr]=makeGaussPulse(flip,lims,...) Create slice selection and 
-%   slice refocusing gradients with the specificed gradient limits 
+%   slice refocusing gradients with the specified gradient limits 
 %   (e.g. amplitude, slew) and taking into account 'centerpos' parameter
 %
 %   See also  Sequence.addBlock

matlab/+mr/makeSincPulse.m

@@ -10,10 +10,10 @@
 %   slice select gradient corresponding to given slice thickness (m).
 %
 %   [rf, gz]=makeSincPulse(flip,lims,...) Create slice selection gradient 
-%   with the specificed gradient limits (e.g. amplitude, slew).
+%   with the specified gradient limits (e.g. amplitude, slew).
 %
 %   [rf, gz, gzr]=makeSincPulse(flip,lims,...) Create slice selection and 
-%   slice refocusing gradients with the specificed gradient limits 
+%   slice refocusing gradients with the specified gradient limits 
 %   (e.g. amplitude, slew) and taking into account 'centerpos' parameter
 %
 %   See also  Sequence.addBlock

matlab/+mr/makeTrapezoid.m

@@ -3,7 +3,7 @@
 %   g=makeTrapezoid(channel, ...) Create trapezoid gradient on
 %   the given channel.
 %
-%   g=makeTrapezoid(channel,lims,...) Create trapezoid with the specificed 
+%   g=makeTrapezoid(channel,lims,...) Create trapezoid with the specified 
 %   gradient limits (e.g. amplitude, slew).
 %
 %   g=makeTrapezoid(...,'Duration',d,'Area',a) Create a

matlab/+mr/simRf.m

@@ -4,7 +4,7 @@
 %   Performs a rapid RF pulse simulation based on the rotation formalism.
 %   The algorithm is optimized by using quaternions to represent rotations. 
 %   The compulsory parameter 'rf' is the Pulseq RF pulse. Optional
-%   parameter 'rephase_factor' is needed in several cases e.g. to correclty 
+%   parameter 'rephase_factor' is needed in several cases e.g. to correctly 
 %   visualize the phase of the magnetization for slice-selective
 %   excitation. Another optional parameter 'prephase_factor' is an 
 %   experimental parameter useful for simulating refocusing pulses or
@@ -63,7 +63,7 @@
 
 shapea = interp1(rf.t, 2*pi*rf.signal.*exp(1i*(rf.phaseOffset+2*pi*rf.freqOffset*rf.t)),T,'linear',0);
 
-% intialize result vectors
+% initialize result vectors
 M_ROT=zeros(size(F)); 
 Z_ROT=zeros(size(F));
 sf=size(F);