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

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+# some abbreviated citations etc
+ignore-regex = Reson Med
+ignore-words-list = te,fo,nd

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+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

01_from_FID_to_PRESS/seq/s04_SE_withBackGrad.m

@@ -70,6 +70,6 @@
 hold on; plot(t_adc,ktraj_adc(1,:),'.'); % and sampling points on the kx-axis
 
 % calculate real TE and TR, etc
-% reported TR will be slighlty higher for Nrep=1 becuse it uses TA instead
+% reported TR will be slightly higher for Nrep=1 because it uses TA instead
 rep = seq.testReport; 
 fprintf([rep{:}]); 

11_from_GRE_to_EPI/recon/r02_2DEPI.m

@@ -38,8 +38,8 @@
     rawdata = double(twix_obj.image.unsorted());
 end
 
-%% if necessary re-tune the trajectory delay to supress ghosting
-traj_recon_delay=0.0e-6;%3.23e-6;%-1e-6;%3.90e-6;%-1.03e-6; % adjust this parameter to supress ghosting (negative allowed) (our trio -1.0e-6, prisma +3.9e-6; avanto +3.88)
+%% if necessary re-tune the trajectory delay to suppress ghosting
+traj_recon_delay=0.0e-6;%3.23e-6;%-1e-6;%3.90e-6;%-1.03e-6; % adjust this parameter to suppress ghosting (negative allowed) (our trio -1.0e-6, prisma +3.9e-6; avanto +3.88)
 [ktraj_adc, t_adc, ktraj, t_ktraj, t_excitation, t_refocusing] = seq.calculateKspacePP('trajectory_delay', traj_recon_delay);
 %[ktraj_adc, ktraj, t_excitation, t_refocusing, t_adc] = seq.calculateKspace('trajectory_delay', traj_recon_delay);
 %ktraj_adc_nodelay=seq.calculateKspace('trajectory_delay', 10e-6);

11_from_GRE_to_EPI/seq/s05_EchoPlanarImaging.m

@@ -11,7 +11,7 @@
 %TR=21e-3;                      % ignore TR, go as fast as possible
 %TE=60e-3;                      % ignore TE, go as fast as possible
 % TODO: run this EPI sequence with and without PE, to calibrate the delay
-% TODO: change MaxGrad/MaxSlew/roDuration to see what happends to the
+% TODO: change MaxGrad/MaxSlew/roDuration to see what happens to the
 % stimulation (e.g. 80/200/500)
 
 % more in-depth parameters
@@ -34,7 +34,7 @@
 blip_dur = ceil(2*sqrt(deltak/sys.maxSlew)/sys.gradRasterTime/2)*sys.gradRasterTime*2; % we round-up the duration to 2x the gradient raster time
 gyBlip = mr.makeTrapezoid('y',sys,'Area',-deltak,'Duration',blip_dur); % we use negative blips to save one k-space line on our way towards the k-space center
 
-% readout gradient is a truncated trapezoid with dead times at the beginnig
+% readout gradient is a truncated trapezoid with dead times at the beginning
 % and at the end, each equal to a half of blip_dur
 % the area between the blips should be equal to kWidth
 % we do a two-step calculation: we first increase the area assuming maximum

11_from_GRE_to_EPI/seq/s06_EPI_SingleTraj.m

@@ -34,7 +34,7 @@
 blip_dur = ceil(2*sqrt(deltak/sys.maxSlew)/sys.gradRasterTime/2)*sys.gradRasterTime*2; % we round-up the duration to 2x the gradient raster time
 gyBlip = mr.makeTrapezoid('y',sys,'Area',-deltak,'Duration',blip_dur); % we use negative blips to save one k-space line on our way towards the k-space center
 
-% readout gradient is a truncated trapezoid with dead times at the beginnig
+% readout gradient is a truncated trapezoid with dead times at the beginning
 % and at the end, each equal to a half of blip_dur
 % the area between the blips should be equal to kWidth
 % we do a two-step calculation: we first increase the area assuming maximum

12_Radial_and_nonCartesian/recon/r02_2D_iRadon.m

@@ -86,7 +86,7 @@
 [~,p2]=min(abs(mod(prg_angle-prg_angle(p1)+2*pi,2*pi)-pi)); % look for the projection closest to the opposite to p1 
 figure;plot(abs(data_fft1c(1:end,p1,1)));hold on;plot(abs(data_fft1c(end:-1:1,p2,1))); title('comparing opposite projections');
 
-%% the actuall iRadon transform
+%% the actual iRadon transform
 theta=270-prg_angle/pi*180;
 for c=1:channels
     % the classical (absolute value) transform

12_Radial_and_nonCartesian/recon/r04_radial_delay_calculation.m

@@ -81,7 +81,7 @@
 
 figure; imagesc(angle(cmplx_diff_no_channels));
 
-%% pick the pure X and pure Y differences, plot them and extimate the slope
+%% pick the pure X and pure Y differences, plot them and estimate the slope
 if length(i_pure2)<2
     [~,p2]=min(abs(mod(prg_angle-prg_angle(1)+2*pi,2*pi)-pi)); % look for the projection closest to the opposite to the 1st 
     i_pure1=[1 p2];

12_Radial_and_nonCartesian/seq/s01_CartesianSE.m

@@ -6,7 +6,7 @@
 rfDur1=3e-3;
 rfDur2=1e-3;
 TR=150e-3;
-TE=54e-3; % 20ms still works with the chosen parameters & sysyem props
+TE=54e-3; % 20ms still works with the chosen parameters & system props
 spA=1000; % spoiler area in 1/m (=Hz/m*s) % MZ: need 5000 for my oil phantom
 
 sliceThickness=3e-3;            % slice

12_Radial_and_nonCartesian/seq/s05_FastRadialGradientEcho.m

@@ -34,7 +34,7 @@
 deltak=1/fov;
 gx = mr.makeTrapezoid('x','Amplitude',Nx*deltak/ro_dur,'FlatTime',ceil(ro_dur/sys.gradRasterTime)*sys.gradRasterTime,'system',sys);
 adc = mr.makeAdc(Nx*ro_os,'Duration',ro_dur,'Delay',gx.riseTime,'system',sys);
-gxPre = mr.makeTrapezoid('x','Area',-gx.amplitude*(ro_dur/Nx/ro_os*(Nx*ro_os/2-0.5)+0.5*gx.riseTime),'system',sys); % 0.5 is necessary to acount for the Siemens sampling in the center of the dwell periods
+gxPre = mr.makeTrapezoid('x','Area',-gx.amplitude*(ro_dur/Nx/ro_os*(Nx*ro_os/2-0.5)+0.5*gx.riseTime),'system',sys); % 0.5 is necessary to account for the Siemens sampling in the center of the dwell periods
 % start gxPre at least right after the RF pulse and when possible end it at the same time as the end of the slice refocusing gradient 
 [gxPre,~,~]=mr.align('right', gxPre, 'right', gzComb, 'left', mr.makeDelay(mr.calcDuration(rf)+mr.calcDuration(gxPre)));
 

12_Radial_and_nonCartesian/seq/s06_Spiral.m

@@ -31,7 +31,7 @@
 kRadius = round(Nx/2);
 kSamples=round(2*pi*kRadius)*Oversampling;
 
-% calculate a raw Archimedian spiral trajectory
+% calculate a raw Archimedean spiral trajectory
 clear ka;
 ka(kRadius*kSamples+1)=1i; % init as complex
 for c=0:kRadius*kSamples
@@ -84,7 +84,7 @@
 adcSegments=round(adcSamplesDesired/adcSamplesPerSegment);
 adcSamples=adcSegments*adcSamplesPerSegment;
 adcDwell=round(adcTime/adcSamples/100e-9)*100e-9; % on Siemens adcDwell needs to be aligned to 100ns (if my memory serves me right)
-adcSegmentDuration=adcSamplesPerSegment*adcDwell; % with the 100 samples above and the 100ns alignment we automatically fullfill the segment alignment requirement
+adcSegmentDuration=adcSamplesPerSegment*adcDwell; % with the 100 samples above and the 100ns alignment we automatically fulfill the segment alignment requirement
 if mod(adcSegmentDuration, sys.gradRasterTime)>eps 
     error('ADC segmentation model results in incorrect segment duration');
 end
@@ -94,7 +94,7 @@
 adc = mr.makeAdc(adcSamples,'Dwell',adcDwell,'Delay',mr.calcDuration(gzReph));%lims.adcDeadTime);
 
 % extend spiral_grad_shape by repeating the last sample
-% this is needed to accomodate for the ADC tuning delay
+% this is needed to accommodate for the ADC tuning delay
 spiral_grad_shape = [spiral_grad_shape spiral_grad_shape(:,end)];
 
 % readout grad 
@@ -110,7 +110,7 @@
 % extends past the end of the trajectory (these points will have to be
 % discarded in the reconstruction, which is no problem). However, the
 % ramp-down parts and the Z-spoiler now have to be added to the readout
-% block otherwise there will be a gap inbetween
+% block otherwise there will be a gap between
 % gz_spoil.delay=mr.calcDuration(gx);
 % gx_spoil.delay=gz_spoil.delay;
 % gy_spoil.delay=gz_spoil.delay;