Merge branch 'develop'

Sync'd .m files in toppe.* and toppe.utils.* with UM gitlab repo (master branch)

+toppe/+utils/coppe.m

@@ -1,11 +1,46 @@
+function coppe(varargin)
+% function coppe(varargin)
+%
+% Load data for one echo (or all) from Pfile, EXCEPT dabslice=0 slot (which can contain corrupt data).
+%
+% Input options:
+%  target          which scanner to copy pulse sequence to
+%                  options: 'inside', 'outside'
+%
 % Packages toppe files into toppe-scanfiles.tgz, then copies it to the scanner
-% Assumes you have SSH keys set up to log into romero
-% Pretty much for UM fMRI lab use only...
+% Assumes you have SSH keys set up to log into romero/toro
+% For UM fMRI lab use only...
+
+import toppe.utils.*
+
+arg.target        = 'inside'; % Default to inside scanner
+arg = vararg_pair(arg, varargin);
 
 fprintf('Making archive...');
 [~,~] = system('tar czf toppe-scanfiles.tgz modules.txt scanloop.txt *.mod'); fprintf('done!\n');
-fprintf('Copying to romero...');
-[~,~] = system('scp toppe-scanfiles.tgz fmrilab@romero:~/amos/'); fprintf('done!\n');
-fprintf('Copying to scanner...');
-[~,~] = system('ssh -q fmrilab@romero "~/amos/pushtoppefiles"'); fprintf('done!\n');
-disp('Ready to scan.');
+
+try
+    switch arg.target
+        case 'inside'
+            fprintf('Copying to romero...');
+            [~,~] = system('scp toppe-scanfiles.tgz fmrilab@romero:~/amos/'); fprintf('done!\n');
+            fprintf('Copying to scanner...');
+            [~,~] = system('ssh -q fmrilab@romero "~/amos/pushtoppefiles"'); fprintf('done!\n');
+
+        case 'outside'
+            fprintf('Copying to toro...');
+            [~,~] = system('scp toppe-scanfiles.tgz fmrilab@toro:~/tmp_amos/'); fprintf('done!\n');
+            fprintf('Copying to scanner...');
+            [~,~] = system('ssh -q fmrilab@toro "~/tmp_amos/pushtoppefiles"'); fprintf('done!\n');
+        otherwise
+            fprintf('Invalid target, valid targets are ''inside'' or ''outside''.\n');
+    end
+    disp('Files sucessfully copied. Finding # of slices...');
+    scanloop_struc = importdata('scanloop.txt');
+	scanloop_struc_data = scanloop_struc.data;
+	max_sli = scanloop_struc_data(2);
+    fprintf('Set # of slices on scanner to %d.\n',max_sli+1);
+    disp('Ready to scan.');
+catch
+    fprintf('\n...failed. Not ready to scan.\n');
+end

+toppe/+utils/fail.m

@@ -1,16 +1,16 @@
  function fail(varargin)
-%function fail(varargin)
+%|function fail(varargin)
 %|
 %| fail with concise but informative error message.
 %| the motivation for this routine is that sometimes matlab's error command
 %| annoyingly does not tell the file/line where the error occured.
 %| this call ensures that the file/line is always displayed.
 
-[name, line] = toppe.utils.caller_name(1);
-if isempty(varargin)
-	toppe.utils.printf('Fail: %s %d', name, line)
+[name line] = caller_name(1);
+if length(varargin)
+	printf(['Fail: %s %d: ' varargin{1}], name, line, varargin{2:end})
 else
-	toppe.utils.printf(['Fail: %s %d: ' varargin{1}], name, line, varargin{2:end})
+	printf(['Fail: %s %d'], name, line)
 end
 %error fail
 evalin('caller', 'error(''!'')')

+toppe/+utils/getSTFRtiming.m

@@ -0,0 +1,73 @@
+function [Tfree Tg TE] = getSTFRtiming(TEro, varargin)
+% function [Tfree Tg TE] = getSTFRtiming(TEro, varargin)
+%
+% Calculate TR/Tfree/Tg/TE for an STFR sequence. 
+% Sequence is assumed to consist of tipdown-readout-tipup-spoiler modules.
+%
+% The file 'modules.txt' must exist in the current folder, and must contain the .mod files 
+% passed to this function.
+%
+% NB! Overwrites scanloop.txt in current folder.
+%
+% Inputs:
+%  TEro      double     Time from beginning of readout to echo (ms)
+% Input options:
+%  tipdown   [string]   .mod file name containing tipdown excitation pulse. Default: 'tipdown.mod'
+%  readout   [string]   .mod file containing readout. Default: 'readout.mod'
+%  tipup     [string]   .mod file name containing tipup excitation pulse. Default: 'tipup.mod'
+%  sys       struct     System hardware specs. See toppe.systemspecs. Default: sys = toppe.systemspecs();
+%
+% Outputs:
+%  TR        double     Sequence TR (ms)
+%  Tfree     double     Time from peak of tipdown pulse to peak of tipup pulse (ms)
+%  Tg        double     Time from peak of tipup pulse to peak of tipdown pulse (ms)
+%  TE        double     Time to echo (ms)
+%
+% Example:
+% >> [~,~,~,~,~,hdrints] = toppe.readmod('readout.mod');
+% >> sys = toppe.systemspecs();
+% >> TEro = 1e-3*(sys.toppe.start_core_daq + sys.toppe.daqdel + hdrints(3)*4);  % ms
+% >> [TR, Tfree, Tg, TE] = toppe.utils.getSTFRtiming(TEro, 'tipdown', 'tipdown,1.mod', 'readout', 'readout,1.mod', 'tipup', 'tipup,1.mod', 'spoiler', 'spoiler,1.mod');
+
+
+% defaults
+arg.tipdown = 'tipdown.mod';
+arg.readout = 'readout.mod';
+arg.tipup   = 'tipup.mod';
+arg.spoiler = 'spoiler.mod';
+arg.system     = toppe.systemspecs();
+
+% parse inputs
+arg = toppe.utils.vararg_pair(arg, varargin);
+
+dt = 4e-3;    % ms
+
+% write scanloop.txt
+toppe.write2loop('setup');
+toppe.write2loop(arg.tipdown);
+toppe.write2loop(arg.readout);
+toppe.write2loop(arg.tipup);
+toppe.write2loop(arg.spoiler);
+toppe.write2loop('finish');
+
+% Tfree
+rf = toppe.plotseq(1, 1, 'doDisplay', false, 'system', arg.system);
+n1 = length(rf);                                 % length of tipdown 
+rf = toppe.plotseq(2, 3, 'doDisplay', false, 'system', arg.system);
+n2 = length(rf);                                 % length of readout+tipup 
+rf = toppe.plotseq(1, 3, 'doDisplay', false, 'system', arg.system);
+I = find(abs(rf(1:n1))==max(abs(rf(1:n1))));
+itipdown = I(1);                                    % the peak can contain more than one sample
+I = find(abs(rf(n1:end))==max(abs(rf(n1:end))));
+itipup = I(1) + n1;                               
+Tfree = dt*(itipup-itipdown);
+
+tipdown.dur = dt*n1;            % ms
+tipdown.tpeak = dt*itipdown;    % ms
+
+% Tg
+rf = toppe.plotseq(1, 4, 'doDisplay', false, 'system', arg.system);
+Tg = dt*length(rf) - Tfree;
+
+% TE
+TE = (tipdown.dur-tipdown.tpeak) + TEro;

+toppe/+utils/getsedelays.m

@@ -0,0 +1,50 @@
+function [delay90 delay180] = getsedelays(tipdown, refocus, readout, te)
+% Calculate delays needed to achieve a desired TE in a spin-echo train.
+% Sequence is assumed to consist of tipdown-refocus-readout-refocus-readout-refocus...
+
+% Inputs:
+%  tipdown   [string]   .mod file name containing 90 degree excitation pulse
+%  refocus   [string]   .mod file containing 180 refocusing pulse
+%  readout   [string]   .mod file containing readout
+%  te        [1 1]      desired TE (ms)
+%
+% Outputs:
+%  delay90   [1 1]   (ms). Apply after 90 pulse
+%  delay180  [1 1]   (ms). Apply before AND after 180 pulses
+%
+
+dt = 4e-3;    % ms
+
+% get minimum TE
+toppe.write2loop('setup');
+toppe.write2loop(tipdown);
+toppe.write2loop(refocus);
+toppe.write2loop(readout);
+toppe.write2loop(refocus);
+toppe.write2loop('finish');
+minsep180 = toppe.getTRtime(2,3)*1e3;     % ms. Minimum separation between 180 pulses.
+
+% return required delay of 180 pulse (to achieve desired TE)
+if minsep180 > te
+	error('Minimum separation between 180 refocusing pulses exceeds requested TE');
+else
+	delay180 = (te-minsep180)/2;
+end
+
+% get separation of 90 pulse and first 180 pulse
+rf = toppe.plotseq(1, 1, 'doDisplay', false);
+n1 = length(rf);                                 % length of 90 module
+rf = toppe.plotseq(2, 2, 'doDisplay', false);
+n2 = length(rf);                                 % length of spin-echo module
+
+rf = toppe.plotseq(1, 2, 'doDisplay', false);
+i90 = find(abs(rf(1:n1))==max(abs(rf(1:n1))));
+i90 = i90(1);                                    % the peak can contain more than one sample
+I = find(abs(rf(n1:end))==max(abs(rf(n1:end))));
+i180 = I(1) + n1;                               
+minsep90180 = dt*(i180-i90);
+if minsep90180 > te/2
+	error('Minimum separation between 90 and first 180 pulse exceeds requested TE');
+else
+	delay90 = te/2 - minsep90180;
+end

+toppe/+utils/ift3.m

@@ -8,6 +8,8 @@
 %  >> size(D) = [64 64 16];    ims = ift3(D, 'type', 2d);          % 16 receive coils; returns multi-coil 2D images
 %  >> size(D) = [64 64 20];    ims = ift3(D, 'dozfft', false);    % does not do ift along kz; returns 3D image
 %
+% $Id: ift3.m,v 1.4 2018/10/26 21:46:41 jfnielse Exp $
+% $Source: /export/home/jfnielse/Private/cvs/projects/psd/toppe/matlab/+toppe/+utils/ift3.m,v $
 
 import toppe.*
 import toppe.utils.*

+toppe/+utils/makegre.m

@@ -13,7 +13,7 @@
 %  system      struct specifying system info, see systemspecs.m
 %  ofname      Output file name. Default: 'readout.mod'
 %  extrafiles  [bool] If true, writes z phase-encode and spoiler to separate .mod files.
-%  slewDerate
+%  slewDerate  Reduce slew rate by this factor during prewinders/crushers
 
 zres = zres*10;   % mm
 
@@ -73,7 +73,11 @@
 if arg.ncycles > 0
 	areacrush = sum(gcrush)*dt*1e-3;   % G/cm*sec
 	arearo = sum([gxprew ramp gxro fliplr(ramp)])*dt*1e-3;
-	bridge = mybridged(areacrush-arearo,gxro(end), mxg, arg.slewDerate*mxs/sqrt(3)*1e3);  
+	if areacrush > arearo
+		bridge = mybridged(areacrush-arearo,gxro(end), mxg, arg.slewDerate*mxs/sqrt(3)*1e3);  
+	else
+		bridge = [];
+	end
 	gx = [gxprew ramp gxro bridge fliplr(ramp)];
 else
 	gx = [ramp gxro fliplr(ramp)];