StitchEM/W005.m at master · talmo/StitchEM · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
%% Configuration
% Wafer and sections
waferpath('/mnt/data0/ashwin/07122012/S2-W005')

% Analyze path
info = get_path_info(waferpath);
status.wafer = info.wafer;
status.pipeline_script = mfilename;
sec_nums = info.sec_nums;

% Skip sections
%sec_nums(103) = []; % skip

% Load default parameters
default_params

%% Custom per-section parameters
% Note: The index of params corresponds to the actual section number.
%
% Example:
%   => Change the NNR MaxRatio of section 38:
%   params(38).z.NNR.MaxRatio = 0.8;
%
%   => Set the max match error for sections 10 to 15 to 2000:
%   params(10).z.max_match_error = 2000; % change section 10's parameters
%   [params(11:15).z] = deal(params(10).z); % copy it to sections 11-15
%       Or:
%   for s=10:15; params(s).z.max_match_error = 2000; end

% S2-W005
% XY
params(35).xy = xy_presets.grid_align;
params(56).xy.max_match_error = inf;

% Z
params(4).z.max_match_error = inf;
params(5).z.max_match_error = inf;
params(8).z.max_match_error = inf;
params(9).z.max_match_error = inf;
params(10).z.max_match_error = inf;
params(11).z.max_match_error = inf;
params(15).z.max_match_error = inf;
params(20).z.max_match_error = inf;
params(21).z.max_match_error = inf;
params(25).z.max_match_error = inf;
params(26).z.max_match_error = inf;
params(27).z.max_match_error = inf;
params(28).z.max_match_error = inf;
params(29).z.max_match_error = inf;
params(32).z.max_match_error = inf;
for s=33:length(params); params(s).z.max_match_error = inf; end

%% Run alignment
try
    align_stack_xy
    align_stack_z
catch alignment_error
    troubleshoot
end