Update ir_mex_build to build penalty_mex file

ir_mex_build.m

@@ -12,5 +12,6 @@
 
 ir_mex_build_mri
 ir_mex_build_table
+irt_mex_make
 
 % todo: ir_mex_build_penal

mex/src/irt_mex_make.m

@@ -1,11 +1,11 @@
 % irt_mex_make.m
 
 if ispc
-	cd penalty
-	mex penalty_mex.c mexarg.c 'penalty,diff.c' -DIs_pc -DMmex -outdir ../v7
-	cd ..
+	cd mex/src/penalty
+    mex penalty_mex.c mexarg.c 'penalty,diff.c' -DIs_pc -DMmex -outdir ../../local
+	cd ../../..
 else
-	cd penalty
-	mex -v penalty_mex.c mexarg.c 'penalty,diff.c' -DMmex -outdir ../v7
-	cd ..
+	cd mex/src/penalty
+    mex -v penalty_mex.c '../def/mexarg.c' 'penalty,diff.c' -I'../def/' -DMmex -outdir ../../local
+	cd ../../..
 end

setup.m

@@ -29,6 +29,11 @@
 	irtdir = [irtdir filesep];
 end
 
+if ~exist([irtdir 'mex/local'], 'dir')
+    disp(sprintf('The directory "%s" does not exist. Creating it now.', [irtdir 'mex/local']))
+    mkdir([irtdir 'mex/local']);
+end
+
 list = {...
 'align', ...		% image registration
 'align/mex', ...	% image registration mex files
@@ -41,6 +46,8 @@
 'fbp', ...		% FBP (filtered backprojection) code
 'general', ...		% generic image reconstruction
 'graph', ...		% graphics routines
+'mex/local', ... % MEX files compiled for local OS/CPU
+'mex/src', ... % MEX source code for irt_mex_make.m
 'mri', ...		% MRI reconstruction
 'mri/fieldmap', ...	% MRI B0 field map estimation
 'mri-rf/yip-spsp', ...	% MRI RF pulse design
@@ -70,8 +77,10 @@
 % e.g., 7.3 and running on earlier 7.0 won't work.
 % If you have mex problems, comment out the following line.
 % Much of the toolbox will work without mex, just slower.
+addpath([irtdir 'mex/local']) % must precede "mex/v7"
 addpath([irtdir 'mex/v7']);
 
+disp('NOTE: Previous irt versions expected MEX files in "mex/v7".')
 
 % do not add the paths below if you are using Matlab!
 if ir_is_octave