Skip to content

Commit b4a62df

Browse files
adamltayloradamltaylor
committed
Moved fix_line_shift_in_place_for_sample.m into mouselight_toolbox
1 parent bc8efd2 commit b4a62df

File tree

1 file changed

+119
-0
lines changed

1 file changed

+119
-0
lines changed

‎line-fix/fix_line_shift_in_place_for_sample.m

+119
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,119 @@
1+
function relative_path_from_tile_index = fix_line_shift_in_place_for_sample(...
2+
tile_root_path, sample_memo_folder_path, do_use_bqueue, do_actually_submit, do_run_in_debug_mode)
3+
4+
% % Build an index of the paths to raw tiles
5+
% sample_tag = '2021-10-19' ;
6+
% analysis_tag = 'get-stragglers' ;
7+
% raw_tiles_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/data/%s/Tiling', sample_tag) ;
8+
% script_folder_path = fileparts(mfilename('fullpath')) ;
9+
% sample_memo_folder_path = fullfile(script_folder_path, 'memos', sample_tag) ;
10+
% analysis_memo_folder_path = fullfile(sample_memo_folder_path, analysis_tag) ;
11+
% %line_fix_path = fullfile(analysis_memo_folder_path, 'stage_1_line_fix_output') ;
12+
% line_fix_path = sprintf('/nrs/mouselight/pipeline_output/%s/stage_1_line_fix_output', sample_tag) ;
13+
% do_write_ancillary_files = true ;
14+
15+
% Set up the par pool
16+
use_this_fraction_of_cores(1) ;
17+
18+
% Build the tile index
19+
do_force_computation = false ;
20+
raw_tile_index = compute_or_read_from_memo(sample_memo_folder_path, ...
21+
'raw-tile-index', ...
22+
@()(build_raw_tile_index(tile_root_path)), ...
23+
do_force_computation) ;
24+
%tile_index_from_tile_ijk1 = raw_tile_index.tile_index_from_tile_ijk1 ;
25+
%ijk1_from_tile_index = raw_tile_index.ijk1_from_tile_index ;
26+
%xyz_from_tile_index = raw_tile_index.xyz_from_tile_index ;
27+
relative_path_from_tile_index = raw_tile_index.relative_path_from_tile_index ;
28+
%raw_tile_map_shape = size(tile_index_from_tile_ijk1)
29+
tile_count = length(relative_path_from_tile_index)
30+
31+
% Read the original sample metadata
32+
original_sample_metadata = read_original_sample_metadata(tile_root_path) ;
33+
34+
35+
%
36+
% Figure out which tiles need to be run
37+
%
38+
39+
fprintf('Determining which of the %d tiles need to be run...\n', tile_count) ;
40+
is_to_be_run_from_tile_index = true(tile_count, 1) ;
41+
% if do_force_computation ,
42+
% is_to_be_run_from_tile_index = true(tile_count, 1) ;
43+
% else
44+
% is_to_be_run_from_tile_index = true(tile_count,1) ;
45+
% pbo = progress_bar_object(tile_count) ;
46+
% for tile_index = 1 : tile_count
47+
% tile_relative_path = relative_path_from_tile_index{tile_index} ;
48+
% is_to_be_run = ...
49+
% ~exist(fullfile(line_fix_path,tile_relative_path,'Xlineshift.txt'), 'file') ;
50+
% is_to_be_run_from_tile_index(tile_index) = is_to_be_run ;
51+
% pbo.update() ; %#ok<PFBNS>
52+
% end
53+
% end
54+
fprintf('Done determining which of the %d tiles need to be run.\n', tile_count) ;
55+
tile_index_from_tile_to_be_run_index = find(is_to_be_run_from_tile_index) ;
56+
relative_path_from_tile_to_be_run_index = relative_path_from_tile_index(is_to_be_run_from_tile_index) ;
57+
tile_to_be_run_count = length(tile_index_from_tile_to_be_run_index)
58+
59+
60+
%
61+
% Run line-fix on all tiles
62+
%
63+
64+
% Create the bqueue
65+
max_running_slot_count = 800 ;
66+
bsub_option_string = '-P mouselight -J line-fix' ;
67+
slots_per_job = 2 ;
68+
stdouterr_file_path = '' ; % will go to /dev/null
69+
70+
if do_use_bqueue ,
71+
fprintf('Queuing line-fixing on %d tiles...\n', tile_to_be_run_count) ;
72+
bqueue = bqueue_type(do_actually_submit, max_running_slot_count) ;
73+
pbo = progress_bar_object(tile_to_be_run_count) ;
74+
for tile_to_be_run_index = 1 : tile_to_be_run_count ,
75+
tile_relative_path = relative_path_from_tile_to_be_run_index{tile_to_be_run_index} ;
76+
%output_folder_path = fullfile(line_fix_path, tile_relative_path) ;
77+
%ensure_folder_exists(output_folder_path) ; % so stdout has somewhere to go
78+
%stdouterr_file_path = fullfile(output_folder_path, 'stdouterr-run-2.txt') ;
79+
bqueue.enqueue(slots_per_job, stdouterr_file_path, bsub_option_string, ...
80+
@fix_line_shift_in_place, ...
81+
tile_root_path, ...
82+
tile_relative_path, ...
83+
original_sample_metadata, ...
84+
do_run_in_debug_mode) ;
85+
pbo.update() ;
86+
end
87+
fprintf('Done queuing line-fixing on %d tiles.\n\n', tile_to_be_run_count) ;
88+
89+
fprintf('Running queue on %d tiles...\n', length(bqueue.job_ids)) ;
90+
maximum_wait_time = inf ;
91+
do_show_progress_bar = true ;
92+
tic_id = tic() ;
93+
job_statuses = bqueue.run(maximum_wait_time, do_show_progress_bar) ;
94+
toc(tic_id)
95+
fprintf('Done running queue on %d tiles.\n', length(bqueue.job_ids)) ;
96+
job_statuses
97+
successful_job_count = sum(job_statuses==1)
98+
else
99+
fprintf('Running in-place line-fixing on %d tiles...\n', tile_to_be_run_count) ;
100+
pbo = progress_bar_object(tile_to_be_run_count) ;
101+
for tile_to_be_run_index = 1 : tile_to_be_run_count ,
102+
tile_relative_path = relative_path_from_tile_to_be_run_index{tile_to_be_run_index} ;
103+
fix_line_shift_in_place( ...
104+
tile_root_path, ...
105+
tile_relative_path, ...
106+
original_sample_metadata, ...
107+
do_run_in_debug_mode) ;
108+
pbo.update() ;
109+
end
110+
fprintf('Done running in-place line-fixing on %d tiles.\n\n', tile_to_be_run_count) ;
111+
112+
end
113+
114+
% Finally, convert the original sample metadata to the sample metadata,
115+
% overwriting the existing file if needed.
116+
% This makes it easy to tell if a sample has been line-shifted.
117+
post_line_fix_sample_metadata = post_line_fix_sample_metadata_from_original_sample_metadata(original_sample_metadata) ;
118+
write_post_line_fix_sample_metadata(tile_root_path, post_line_fix_sample_metadata) ;
119+
end

0 commit comments

Comments
 (0)