arrays - MatLab Bottleneck -

i working big arrays (~6x40million) , code showing great bottlenecks. experienced programming in matlab, don't know inner processes (like memory , such...).

my code looks follows(just essentials, of course variables initialized, specially arrays in loops, don't want bomb code ):

first read file,

 disp('point cloud import , subsampling')     tic     fid=fopen(strcat(name,'.dat'));     c=textscan(fid, '%d%d%f%f%f%d'); %<= big!     fclose(fid); 

then create arrays out of contents,

    y=c{1}(1:subsampling:end)/subsampling;     x=c{2}(1:subsampling:end)/subsampling;     %... , on other rows          clear c %no 1 wants 400+ millon doubles lying around. 

and clear cell array (1), , create images , arrays new values

for i=1:length(x)      pcimage(y(i)+subsize(1)-maxy+1,x(i)+1-minx)=reflectanse(i);          pixelcoordinates(y(i)+subsize(1)-maxy+1,x(i)+1-minx,:)=coordinates(i,:);  end toc 

everything runs more or less smoothly until here, manipulate arrays

disp('overlap alignment')    tic      pcimage=pcimage(:,[1:maxx/2-overlap,maxx/2:end-overlap]); %-30 overlap?     pixelcoordinates=pixelcoordinates(:,[1:maxx/2-overlap,maxx/2:end-overlap],:);     sphere=sphere(:,[1:maxx/2-overlap,maxx/2:end-overlap],:);  toc  

and big bottleneck, gets worst @ next step

disp('planar view , point cloud matching')    tic     compimage=zeros(max(subsize(1),pcsize(1)),max(subsize(2),pcsize(2)),3);     compimage(1:subsize(1),1:subsize(2),2)=subimage; %exportimage cyan    compimage(1:subsize(1),1:subsize(2),3)=subimage;    compimage(1:pcsize(1),1:pcsize(2),1)=pcimage; %pointcloudimage red    toc 

output

point cloud import , subsampling

elapsed time 181.157182 seconds.

overlap alignment

elapsed time 408.750932 seconds.

planar view , point cloud matching

elapsed time 719.383807 seconds.

my questions are: clearing unused objects c in 1 have effect? (it doesn't seem that)

am overseeing other important mechanisms or rules of thumb, or whole thing , supposed happen this?

when subsref used, matlab makes copy of sub referenced elements. may costly large arrays. faster catenate vectors like

res = [a,b,c]; 

this not possible current code written above, if code modified make work, may save time.

edit multi-dimensional arrays need use cat

compimage = cat(dim,subimage,subimage,pcimage); 

where dim 3 example.