[format] complete reformat of code using miss_hit

Author: fangq

.miss_hit

@@ -0,0 +1,11 @@
+project_root
+
+suppress_rule: "redundant_brackets"
+suppress_rule: "line_length"
+suppress_rule: "file_length"
+suppress_rule: "copyright_notice"
+suppress_rule: "naming_functions"
+suppress_rule: "naming_parameters"
+suppress_rule: "naming_scripts"
+suppress_rule: "unicode"
+indent_function_file_body: false

advancefront.m

@@ -1,4 +1,4 @@
-function [elist,nextfront]=advancefront(edges,loop,elen)
+function [elist, nextfront] = advancefront(edges, loop, elen)
 %
 % [elist,nextfront]=advancefront(edges,loop,elen)
 %
@@ -21,32 +21,34 @@
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-elist=[];
-nextfront=[];
+elist = [];
+nextfront = [];
 
-if(nargin<3) elen=3; end
+if (nargin < 3)
+    elen = 3;
+end
 
-[hasedge, loc]=ismember(loop,edges,'rows');
+[hasedge, loc] = ismember(loop, edges, 'rows');
 
-if(~all(hasedge))
-   error('loop edge is not defined in the mesh');
+if (~all(hasedge))
+    error('loop edge is not defined in the mesh');
 end
 
-nodenum=size(edges,1)/elen;
+nodenum = size(edges, 1) / elen;
 
-elist=unique(mod(loc-1,nodenum))+1;
-nextfront=edges(elist,:);
-for i=1:elen-1
-    nextfront=[nextfront;edges(elist+nodenum*i,:)];
+elist = unique(mod(loc - 1, nodenum)) + 1;
+nextfront = edges(elist, :);
+for i = 1:elen - 1
+    nextfront = [nextfront; edges(elist + nodenum * i, :)];
 end
-nextfront=setdiff(nextfront,loop,'rows');
+nextfront = setdiff(nextfront, loop, 'rows');
 
 % remove reversed edge pairs
-[flag,loc]=ismember(nextfront,nextfront(:,[2 1]),'rows');
-id=find(flag);
-if(~isempty(id))
-    delmark=flag;
-    delmark(loc(find(loc>0)))=1;
-    nextfront(find(delmark),:)=[];
+[flag, loc] = ismember(nextfront, nextfront(:, [2 1]), 'rows');
+id = find(flag);
+if (~isempty(id))
+    delmark = flag;
+    delmark(loc(find(loc > 0))) = 1;
+    nextfront(find(delmark), :) = [];
 end
-nextfront=nextfront(:,[2 1]); % reverse this loop, as it is reversed to the input loop
+nextfront = nextfront(:, [2 1]); % reverse this loop, as it is reversed to the input loop

affinemap.m

@@ -1,4 +1,4 @@
-function [A,b]=affinemap(pfrom,pto)
+function [A, b] = affinemap(pfrom, pto)
 %  [A,b]=affinemap(pfrom,pto)
 %
 %  calculate an affine transform (A matrix and b vector) to map n
@@ -7,7 +7,7 @@
 %  author: Qianqian Fang <q.fang at neu.edu>
 %  date: 12/12/2008
 %
-% parameters: 
+% parameters:
 %      pfrom: nx3 matrix, each row is a 3d point in original space
 %      pto: nx3 matrix, each row is a 3d point in the mapped space
 %
@@ -21,20 +21,20 @@
 %
 % this function is part of "metch" toobox, see COPYING for license
 
-bsubmat=eye(3);
-ptnum=size(pfrom,1);
-if(size(pto,1)~=ptnum)
-        error('two inputs should have the same size');
+bsubmat = eye(3);
+ptnum = size(pfrom, 1);
+if (size(pto, 1) ~= ptnum)
+    error('two inputs should have the same size');
 end
-amat=zeros(ptnum*3,9);
-for i=1:ptnum
-        amat(i*3-2:i*3,:)=kron(bsubmat,pfrom(i,:));
+amat = zeros(ptnum * 3, 9);
+for i = 1:ptnum
+    amat(i * 3 - 2:i * 3, :) = kron(bsubmat, pfrom(i, :));
 end
-amat=[amat,repmat(bsubmat,ptnum,1)];
+amat = [amat, repmat(bsubmat, ptnum, 1)];
 
-bvec=pto';
-bvec=bvec(:);
+bvec = pto';
+bvec = bvec(:);
 
-x=amat\bvec;
-A=reshape(x(1:9),3,3)';
-b=x(end-2:end);
+x = amat \ bvec;
+A = reshape(x(1:9), 3, 3)';
+b = x(end - 2:end);

aos2soa.m

@@ -1,4 +1,4 @@
-function st=aos2soa(starray)
+function st = aos2soa(starray)
 %
 %    st=aos2soa(starray)
 %
@@ -23,18 +23,17 @@
 %    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
 %
 
-
-if(nargin<1 || ~isstruct(starray))
+if (nargin < 1 || ~isstruct(starray))
     error('you must give an array of struct');
 end
 
-if(numel(starray)==1)
-    st=starray;
-    return;
+if (numel(starray) == 1)
+    st = starray;
+    return
 end
 
-st=struct;
-fn=fieldnames(starray);
-for i=1:length(fn)
-    st.(fn{i})=[starray(:).(fn{i})];
-end
+st = struct;
+fn = fieldnames(starray);
+for i = 1:length(fn)
+    st.(fn{i}) = [starray(:).(fn{i})];
+end

barydualmesh.m

@@ -1,4 +1,4 @@
-function [newnode,newelem]=barydualmesh(node,elem,flag)
+function [newnode, newelem] = barydualmesh(node, elem, flag)
 %
 % [newnode,newelem]=barydualmesh(node,elem)
 %
@@ -24,36 +24,28 @@
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-[enodes,eidx]=highordertet(node,elem);               % compute edge-centers
+[enodes, eidx] = highordertet(node, elem);               % compute edge-centers
 
-if(size(elem,2)==3)
-    fnodes=meshcentroid(node,elem);                  % compute face-centers
-    fidx=1:
-    newnode=[enodes;fnodes];
-    newidx=[eidx, fidx+size(enodes,1), (1:size(elem,1))'+(size(enodes,1)+size(fnodes,1))];
-    return;
-end
-
-[fnodes,fidx]=elemfacecenter(node,elem);             % compute face-centers
-c0=meshcentroid(node,elem(:,1:min(size(elem,2),4))); % compute elem-centers
+[fnodes, fidx] = elemfacecenter(node, elem);             % compute face-centers
+c0 = meshcentroid(node, elem(:, 1:min(size(elem, 2), 4))); % compute elem-centers
 
 % concatenated new nodes and their indices
-newnode=[enodes;fnodes;c0];
-newidx=[eidx, fidx+size(enodes,1), (1:size(elem,1))'+(size(enodes,1)+size(fnodes,1))];
+newnode = [enodes; fnodes; c0];
+newidx = [eidx, fidx + size(enodes, 1), (1:size(elem, 1))' + (size(enodes, 1) + size(fnodes, 1))];
 
-newelem=[
-    1 8 11 7
-    2 7 11 9
-    3 9 11 8
-    4 7 11 10
-    5 8 11 10
-    6 9 11 10
-    ];
-newelem=newelem';
-newelem=newidx(:,newelem(:));
-newelem=reshape(newelem,[size(elem,1) 4 6]);
-newelem=permute(newelem,[1 3 2]);
-newelem=reshape(newelem,[size(elem,1)*6 4]);
-if(nargin>2 && ischar(flag) && strcmp(flag,'cell'))
-    newelem=num2cell(newelem,2);
+newelem = [
+           1 8 11 7
+           2 7 11 9
+           3 9 11 8
+           4 7 11 10
+           5 8 11 10
+           6 9 11 10
+          ];
+newelem = newelem';
+newelem = newidx(:, newelem(:));
+newelem = reshape(newelem, [size(elem, 1) 4 6]);
+newelem = permute(newelem, [1 3 2]);
+newelem = reshape(newelem, [size(elem, 1) * 6 4]);
+if (nargin > 2 && ischar(flag) && strcmp(flag, 'cell'))
+    newelem = num2cell(newelem, 2);
 end

bbxflatsegment.m

@@ -1,87 +1,99 @@
-function seg=bbxflatsegment(node,loop)
+function seg = bbxflatsegment(node, loop)
 %
 % seg=bbxflatsegment(node,loop)
 %
-% decompose edge loops into flat segments along the x/y/z 
+% decompose edge loops into flat segments along the x/y/z
 % planes of the bounding box
 %
 % author: Qianqian Fang, <q.fang at neu.edu>
 % date: 2008/04/08
 %
-% input:   
+% input:
 %    node:  x,y,z coordinates of each node of the mesh
 %    loop:  input, a single vector separated by NaN, each segment
-%             is a close-polygon consisted by node IDs 
+%             is a close-polygon consisted by node IDs
 % output:
 %    seg:   output, a single vector separated by NaN, each segment
-%             is a close-polygon on x/y/z plane 
+%             is a close-polygon on x/y/z plane
 %
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-pos=node(loop,:);
+pos = node(loop, :);
 
 % get the bounding box
-mi=min(pos);
-ma=max(pos);
+mi = min(pos);
+ma = max(pos);
 
 % extract nodes on the bounding box
-idx0=find(abs(pos(:,1)-mi(1))<1e-6)';
-idx1=find(abs(pos(:,1)-ma(1))<1e-6)';
+idx0 = find(abs(pos(:, 1) - mi(1)) < 1e-6)';
+idx1 = find(abs(pos(:, 1) - ma(1)) < 1e-6)';
 
-idy0=find(abs(pos(:,2)-mi(2))<1e-6)';
-idy1=find(abs(pos(:,2)-ma(2))<1e-6)';
+idy0 = find(abs(pos(:, 2) - mi(2)) < 1e-6)';
+idy1 = find(abs(pos(:, 2) - ma(2)) < 1e-6)';
 
-idz0=find(abs(pos(:,3)-mi(3))<1e-6)';
-idz1=find(abs(pos(:,3)-ma(3))<1e-6)';
+idz0 = find(abs(pos(:, 3) - mi(3)) < 1e-6)';
+idz1 = find(abs(pos(:, 3) - ma(3)) < 1e-6)';
 
 % need to be more than 3 points to make a flat polygon
 
-if(length(idx0)<=3) idx0=[]; end
-if(length(idx1)<=3) idx1=[]; end
-if(length(idy0)<=3) idy0=[]; end
-if(length(idy1)<=3) idy1=[]; end
-if(length(idz0)<=3) idz0=[]; end
-if(length(idz1)<=3) idz1=[]; end
+if (length(idx0) <= 3)
+    idx0 = [];
+end
+if (length(idx1) <= 3)
+    idx1 = [];
+end
+if (length(idy0) <= 3)
+    idy0 = [];
+end
+if (length(idy1) <= 3)
+    idy1 = [];
+end
+if (length(idz0) <= 3)
+    idz0 = [];
+end
+if (length(idz1) <= 3)
+    idz1 = [];
+end
 
-nn=length(loop);
+nn = length(loop);
 
 % if the original is a flat polygon, return
 
-if(unique(length(idx0))==nn || unique(length(idx1))==nn ...
-  |unique(length(idy0))==nn || unique(length(idy1))==nn ...
-  |unique(length(idz0))==nn || unique(length(idz1))==nn) 
-    seg=loop(:)';
-    return;
+if (unique(length(idx0)) == nn || unique(length(idx1)) == nn || ...
+    unique(length(idy0)) == nn || unique(length(idy1)) == nn || ...
+    unique(length(idz0)) == nn || unique(length(idz1)) == nn)
+    seg = loop(:)';
+    return
 end
 
 % otherwise, find the combination that split the loop
 
-if(length(unique([idx0 idy0 idz0]))==nn)
-   seg= [loop(idx0),nan,loop(idy0),nan,loop(idz0)];
-elseif(length(unique([idx0 idy1 idz0]))==nn)
-   seg= [loop(idx0),nan,loop(idy1),nan,loop(idz0)];
-elseif(length(unique([idx0 idy0 idz1]))==nn)
-   seg= [loop(idx0),nan,loop(idy0),nan,loop(idz1)];
-elseif(length(unique([idx0 idy1 idz1]))==nn)
-   seg= [loop(idx0),nan,loop(idy1),nan,loop(idz1)];
-elseif(length(unique([idx1 idy0 idz0]))==nn)
-   seg= [loop(idx1),nan,loop(idy0),nan,loop(idz0)];
-elseif(length(unique([idx1 idy1 idz0]))==nn)
-   seg= [loop(idx1),nan,loop(idy1),nan,loop(idz0)];
-elseif(length(unique([idx1 idy0 idz1]))==nn)
-   seg= [loop(idx1),nan,loop(idy0),nan,loop(idz1)];
-elseif(length(unique([idx1 idy1 idz1]))==nn)
-   seg= [loop(idx1),nan,loop(idy1),nan,loop(idz1)];
+if (length(unique([idx0 idy0 idz0])) == nn)
+    seg = [loop(idx0), nan, loop(idy0), nan, loop(idz0)];
+elseif (length(unique([idx0 idy1 idz0])) == nn)
+    seg = [loop(idx0), nan, loop(idy1), nan, loop(idz0)];
+elseif (length(unique([idx0 idy0 idz1])) == nn)
+    seg = [loop(idx0), nan, loop(idy0), nan, loop(idz1)];
+elseif (length(unique([idx0 idy1 idz1])) == nn)
+    seg = [loop(idx0), nan, loop(idy1), nan, loop(idz1)];
+elseif (length(unique([idx1 idy0 idz0])) == nn)
+    seg = [loop(idx1), nan, loop(idy0), nan, loop(idz0)];
+elseif (length(unique([idx1 idy1 idz0])) == nn)
+    seg = [loop(idx1), nan, loop(idy1), nan, loop(idz0)];
+elseif (length(unique([idx1 idy0 idz1])) == nn)
+    seg = [loop(idx1), nan, loop(idy0), nan, loop(idz1)];
+elseif (length(unique([idx1 idy1 idz1])) == nn)
+    seg = [loop(idx1), nan, loop(idy1), nan, loop(idz1)];
 else
-    seg=[];
+    seg = [];
 end
 
 % remove pattern [ ... nan nan ...] in the result
 
-if(length(seg) && any(isnan(seg)))
-    id=regexp(sprintf('%d',isnan(seg)),'11');
-    if(length(id))
-        seg(id+1)=[];
+if (length(seg) && any(isnan(seg)))
+    id = regexp(sprintf('%d', isnan(seg)), '11');
+    if (length(id))
+        seg(id + 1) = [];
     end
 end