MATLAB examples update, fix projection default args (#38)

* Remove old interface example
* Fix deafault args on projection
* Fix element integral demos

NOTES.md

@@ -4,19 +4,16 @@
 
  - Investigate `warning C4910` on MSVC - some declspec conflict
  - Look at `fwdsolver_mw.h` instantiation requirements, determine appropriate preprocessor gaurd (e.g. Clang?)
+ - MATLAB QM are always complex, will crash on forward solve with real (NB interleaved API motivation)
  - MATLAB gmsh reader out of date
- - MATLAB complex outputs on QM
  - MATLAB flourescence example performance
- - MATLAB Fix `element_integrals.m` example dimensionality problems
  - Interleaved API permits shallow copy of various inputs in the MATLAB interface to reduce round-trip, exploit
  - Review element types in libfe, some contain unfinished defintions of operators and constants, remove
  - Move semantics for mathlib vectors and matrices
  - Improved initialisation for element entries
  - Check propensity for structural nonzeros viz. direct solvers
- - Resolve versioning 
  - Python interface build assumes Release paths on Windows
  - Default link list after make mesh appears arbitrary, resulting in enormous linklist/qmvec
- - Real qvec on forward solver crash
 
 ## Perfromance
 

script/matlab/examples/element_integrals.m

@@ -38,11 +38,11 @@
 % Now do the same with a numerical quadrature rule
 qwght = 1/6 * [1 1 1];
 qabsc = [1/2,0; 0,1/2; 1/2,1/2]';
-fun = el.ShapeFun(qabsc);
-der = el.ShapeDer(qabsc);
+fun = el.ShapeFun(qabsc);   % nn x np
+der = el.ShapeDer(qabsc');  % nn x d x np
 intf_numeric = zeros(3,1);
 for q=1:3
-    jac = der(:,:,q)*vtx;
+    jac = der(:,:,q)'*vtx;
     v = qwght(q) * det(jac);
     intf_numeric = intf_numeric + v*fun(:,q);
 end
@@ -63,7 +63,7 @@
 % And the numerical quadrature version
 intff_numeric = zeros(3,3);
 for q=1:3
-    jac = der(:,:,q)*vtx;
+    jac = der(:,:,q)'*vtx;
     v = qwght(q) * det(jac);
     intff_numeric = intff_numeric + v * (fun(:,q) * fun(:,q)');
 end
@@ -86,10 +86,10 @@
 % And the numerical quadrature version
 intdd_numeric = zeros(3,3);
 for q=1:3
-    jac = der(:,:,q)*vtx;
+    jac = der(:,:,q)'*vtx;
     ijac = inv(jac);
     v = qwght(q) * det(jac);
-    ider = ijac*der(:,:,q);
+    ider = ijac*der(:,:,q)';
     intdd_numeric = intdd_numeric + v * (ider' * ider);
 end
 

script/matlab/examples/fwd1_aniso3D.m

@@ -1,7 +1,7 @@
 function tmp
 close all
 
-meshdir = '.../meshes/3D/';
+meshdir = '../meshes/3D/';
 hmesh = toastMesh([meshdir 'cyl3.msh']);
 hmesh.ReadQM([meshdir 'cyl_3ring.qm']);
 

script/matlab/toast/toastProject.m

@@ -26,12 +26,14 @@
 % is, unused source-detector combinations are removed from the result.
 
 % Subsititute missing parameters with defaults
-if nargin < 8
-    solver = 'direct';
-elseif nargin < 9
+if nargin < 9
     tol = 1e-10;
 end
 
+if nargin < 8
+    solver = 'direct';   
+end
+
 % Calculate system matrix
 phi = toastFields(hMesh, 0,  qvec, mua, mus, ref, omega, solver, tol, 'auto');