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adamltayloradamltaylor
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Added script for stage 1234 processing
1 parent 571064e commit 615c41a

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‎lpl_process_single_tile.m

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function lpl_process_single_tile(tile_relative_path, raw_root_path, line_fix_root_path, p_map_root_path, landmark_root_path, ...
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do_line_fix, do_force_computation, do_run_in_debug_mode)
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% sample date something like '2021-09-16'
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% tile_relative_path something like '2021-09-17/00/00000'
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% Deal with args
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if ~exist('do_force_computation', 'var') || isempty(do_force_computation) ,
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do_force_computation = false ;
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end
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if ~exist('do_run_in_debug_mode', 'var') || isempty(do_run_in_debug_mode) ,
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do_run_in_debug_mode = false ;
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end
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% % Generate paths to various things
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% raw_root_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/data/%s/Tiling', sample_date) ;
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% line_fix_root_path = sprintf('/nrs/mouselight/pipeline_output/%s/stage_1_line_fix_output', sample_date) ;
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% p_map_root_path = sprintf('/nrs/mouselight/pipeline_output/%s/stage_2_classifier_output', sample_date) ;
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% landmarks_root_path = sprintf('/nrs/mouselight/pipeline_output/%s/stage_3_descriptor_output', sample_date) ;
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% Find the tiles in the raw imagery folder
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raw_imagery_folder_path = fullfile(raw_root_path, tile_relative_path) ;
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[~,day_tile_index_string] = fileparts2(tile_relative_path) ; % e.g. '00000'
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raw_imagery_file_name_template = sprintf('%s-ngc.*.tif', day_tile_index_string) ;
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raw_imagery_file_path_template = fullfile(raw_imagery_folder_path, raw_imagery_file_name_template) ;
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raw_imagery_tile_file_names = simple_dir(raw_imagery_file_path_template) ;
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tile_file_count = length(raw_imagery_tile_file_names) ;
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% Fix the line-shift
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if do_line_fix,
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fix_line_shift(raw_root_path, tile_relative_path, line_fix_root_path, do_force_computation, do_run_in_debug_mode) ;
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end
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% Process each tile in turn
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if do_line_fix ,
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p_map_input_root_path = line_fix_root_path ;
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else
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p_map_input_root_path = raw_root_path ;
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end
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for tile_file_index = 1 : tile_file_count ,
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raw_imagery_tile_file_name = raw_imagery_tile_file_names{tile_file_index} ;
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lpl_process_single_tile_channel(...
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raw_imagery_tile_file_name, tile_relative_path, p_map_input_root_path, p_map_root_path, landmark_root_path) ;
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end
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end

‎lpl_process_single_tile_channel.m

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function lpl_process_single_tile_channel(raw_tile_file_name, tile_relative_path, input_root_path, p_map_root_path, landmarks_root_path, ...
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do_force_computation, do_run_in_debug_mode)
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% Deal with args
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if ~exist('do_force_computation', 'var') || isempty(do_force_computation) ,
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do_force_computation = false ;
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end
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if ~exist('do_run_in_debug_mode', 'var') || isempty(do_run_in_debug_mode) ,
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do_run_in_debug_mode = false ;
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end
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% Compute the p-map file path
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input_file_path = fullfile(input_root_path, tile_relative_path, raw_tile_file_name) ;
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[~,day_tile_index_as_string] = fileparts2(tile_relative_path) ;
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channel_index0_as_string = channel_index0_as_string_from_tile_file_name(raw_tile_file_name) ;
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p_map_file_name = sprintf('%s-prob.%s.h5', day_tile_index_as_string, channel_index0_as_string) ;
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p_map_tile_folder_path = fullfile(p_map_root_path, tile_relative_path) ;
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p_map_file_path = fullfile(p_map_tile_folder_path, p_map_file_name) ;
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% Shell out to run Ilastik
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if do_force_computation || ~exist(p_map_file_path, 'file') ,
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ensure_folder_exists(p_map_tile_folder_path) ;
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%script_path = mfilename('fullpath') ;
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%script_folder_path = fileparts(script_path) ;
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%ilastik_project_path = fullfile(script_folder_path, '/groups/mousebrainmicro/mousebrainmicro/pipeline-systems axon-classifier/axon_uint16.ilp') ;
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ilastik_project_path = '/groups/mousebrainmicro/mousebrainmicro/pipeline-systems/pipeline-a/apps/axon-classifier/axon_uint16.ilp' ;
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IL_PREFIX = '/groups/mousebrainmicro/mousebrainmicro/pipeline-systems/tools/ilastik-1.1.9-Linux' ;
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%IL_PREFIX = '/groups/mousebrainmicro/mousebrainmicro/Software/ilastik-1.3.3post2-Linux' ;
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%IL_PREFIX = '/groups/mousebrainmicro/mousebrainmicro/Software/ilastik-1.3.3-Linux' ;
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output_format = 'hdf5' ;
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%'multipage tiff', 'multipage tiff sequence', 'hdf5'
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python_path = fullfile(IL_PREFIX, 'bin/python') ;
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ilastik_dot_py_path = fullfile(IL_PREFIX, 'ilastik-meta/ilastik/ilastik.py') ;
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%command_line = sprintf(['export LAZYFLOW_THREADS=4 ; ' ...
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% 'export LAZYFLOW_TOTAL_RAM_MB=60000 ; ' ...
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% '"%s" ' ...
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command_line = sprintf(['export LAZYFLOW_THREADS=4 ; ' ...
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'export LAZYFLOW_TOTAL_RAM_MB=60000 ; ' ...
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'"%s" ' ...
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'"%s" ' ...
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'--headless ' ...
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'--readonly 1 ' ...
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'--cutout_subregion="[(None,None,None,0),(None,None,None,1)]" ' ...
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'--project="%s" ' ...
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'--output_filename_format="%s" ' ...
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'--output_format="%s" ' ...
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'"%s"'] , ...
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python_path, ...
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ilastik_dot_py_path, ...
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ilastik_project_path, ...
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p_map_file_path, ...
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output_format, ...
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input_file_path) ;
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fprintf('Ilastik command line: %s\n', command_line) ;
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system_with_error_handling(command_line) ;
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end
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% Generate the landmarks from the p-map
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landmark_file_name = sprintf('%s-desc.%s.txt', day_tile_index_as_string, channel_index0_as_string) ;
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landmark_folder_path = fullfile(landmarks_root_path, tile_relative_path) ;
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landmark_file_path = fullfile(landmark_folder_path, landmark_file_name) ;
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% Make sure the output folder exists
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ensure_folder_exists(landmark_folder_path) ;
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% Run the core code
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siz = '[11 11 11]' ;
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sig1 = '[3.405500 3.405500 3.405500]' ;
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sig2 = '[4.049845 4.049845 4.049845]' ;
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ROI = '[5 1019 5 1531 5 250]' ;
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rt = '4' ;
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exitcode = dogDescriptor(p_map_file_path, landmark_file_path, siz, sig1, sig2, ROI, rt) ;
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if exitcode ~= 0 ,
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error('dogDescriptor() returned a nonzero exit code (%s) when trying to produce output file %s', exitcode, landmark_file_path) ;
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end
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end

‎run_all_tiles_through_1234_stages.m

+159
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% Set up the par pool
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use_this_fraction_of_cores(1) ;
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% Set params for early jobs
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do_use_bsub = false ;
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do_actually_submit = false ;
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max_running_slot_count = inf ;
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bsub_option_string = '-P mouselight -J mouselight-pipeline-123' ;
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slots_per_job = 4 ;
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stdouterr_file_path = '' ; % will go to /dev/null
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% Build the tile index
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raw_tile_index = compute_or_read_from_memo(sample_memo_folder_path, ...
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'raw-tile-index', ...
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@()(build_raw_tile_index(raw_root_path)), ...
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do_force_computation) ;
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tile_index_from_tile_ijk1 = raw_tile_index.tile_index_from_tile_ijk1 ;
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ijk1_from_tile_index = raw_tile_index.ijk1_from_tile_index ;
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xyz_from_tile_index = raw_tile_index.xyz_from_tile_index ;
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relative_path_from_tile_index = raw_tile_index.relative_path_from_tile_index ;
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raw_tile_map_shape = size(tile_index_from_tile_ijk1)
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tile_count = length(relative_path_from_tile_index)
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%
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% Figure out which tiles need to be run
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%
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%is_to_be_run_from_tile_index = false(tile_count, 1) ;
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%is_to_be_run_from_tile_index(1:20) = true ;
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fprintf('Determining which of the %d tiles need to be LPLed...\n', tile_count) ;
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if do_force_computation ,
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is_to_be_run_from_tile_index = true(tile_count, 1) ;
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else
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is_to_be_run_from_tile_index = true(tile_count,1) ;
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parfor_progress(tile_count) ;
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parfor tile_index = 1 : tile_count
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tile_relative_path = relative_path_from_tile_index{tile_index} ;
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channel_0_tile_file_name = landmark_file_name_from_tile_relative_path(tile_relative_path, 0) ;
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channel_0_tile_file_path = fullfile(landmark_root_path, tile_relative_path, channel_0_tile_file_name) ;
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channel_1_tile_file_name = landmark_file_name_from_tile_relative_path(tile_relative_path, 1) ;
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channel_1_tile_file_path = fullfile(landmark_root_path, tile_relative_path, channel_1_tile_file_name) ;
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is_to_be_run = ...
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~(exist(channel_0_tile_file_path, 'file') && exist(channel_1_tile_file_path, 'file')) ;
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is_to_be_run_from_tile_index(tile_index) = is_to_be_run ;
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parfor_progress() ;
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end
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parfor_progress(0) ;
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end
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fprintf('Done determining which of the %d tiles need to be LPLed.\n', tile_count) ;
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tile_index_from_tile_to_be_run_index = find(is_to_be_run_from_tile_index) ;
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relative_path_from_tile_to_be_run_index = relative_path_from_tile_index(is_to_be_run_from_tile_index) ;
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tile_to_be_run_count = length(tile_index_from_tile_to_be_run_index)
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57+
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%
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% Run stages 123 on all tiles
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%
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% Create the bqueue
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if do_use_bsub ,
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fprintf('Queueing LPL on %d tiles...\n', tile_to_be_run_count) ;
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bqueue = bqueue_type(do_actually_submit, max_running_slot_count) ;
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parfor_progress(tile_to_be_run_count) ;
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for tile_to_be_run_index = 1 : tile_to_be_run_count ,
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tile_relative_path = relative_path_from_tile_to_be_run_index{tile_to_be_run_index} ;
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%output_folder_path = fullfile(line_fix_path, tile_relative_path) ;
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%ensure_folder_exists(output_folder_path) ; % so stdout has somewhere to go
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%stdouterr_file_path = fullfile(output_folder_path, 'stdouterr-run-2.txt') ;
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bqueue.enqueue(slots_per_job, stdouterr_file_path, bsub_option_string, ...
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@lpl_process_single_tile, ...
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tile_relative_path, ...
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raw_root_path, ...
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line_fix_root_path, ...
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p_map_root_path, ...
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landmark_root_path, ...
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do_line_fix, ...
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do_force_computation) ;
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parfor_progress() ;
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end
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parfor_progress(0) ;
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fprintf('Done queueing LPL on %d tiles.\n\n', tile_to_be_run_count) ;
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fprintf('LPLing queue on %d tiles...\n', length(bqueue.job_ids)) ;
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maximum_wait_time = inf ;
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do_show_progress_bar = true ;
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tic_id = tic() ;
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job_statuses = bqueue.run(maximum_wait_time, do_show_progress_bar) ;
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toc(tic_id)
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fprintf('Done LPLing queue on %d tiles.\n', length(bqueue.job_ids)) ;
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job_statuses
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successful_job_count = sum(job_statuses==1)
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else
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% Useful for debugging
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parfor_progress(tile_to_be_run_count) ;
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for tile_to_be_run_index = 1 : tile_to_be_run_count ,
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tile_relative_path = relative_path_from_tile_to_be_run_index{tile_to_be_run_index} ;
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%output_folder_path = fullfile(line_fix_path, tile_relative_path) ;
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%ensure_folder_exists(output_folder_path) ; % so stdout has somewhere to go
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%stdouterr_file_path = fullfile(output_folder_path, 'stdouterr-run-2.txt') ;
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lpl_process_single_tile( ...
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tile_relative_path, ...
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raw_root_path, ...
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line_fix_root_path, ...
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p_map_root_path, ...
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landmark_root_path, ...
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do_line_fix, ...
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do_force_computation) ;
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parfor_progress() ;
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end
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parfor_progress(0) ;
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end
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%
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% Run stage 4 (landmark matching)
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% We bqueue up a single job that will use 48 cores
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%
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% New params for bjobs
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do_use_bsub = true ;
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do_actually_submit = true ;
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max_running_slot_count = inf ;
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bsub_option_string = '-P mouselight -J mouselight-landmark-matching' ;
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slots_per_job = 48 ;
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stdouterr_file_path = fullfile(script_folder_path, 'mouselight-landmark-matching.out.txt') ;
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% Create the bqueue
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if do_use_bsub ,
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fprintf('Running landmark-matching (as single bsub job)...\n') ;
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bqueue = bqueue_type(do_actually_submit, max_running_slot_count) ;
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bqueue.enqueue(slots_per_job, stdouterr_file_path, bsub_option_string, ...
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@landmark_match_all_tiles_in_z, ...
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raw_root_path, ...
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sample_memo_folder_path, ...
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landmark_root_path, ...
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z_point_match_root_path, ...
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do_force_computation) ;
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maximum_wait_time = inf ;
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do_show_progress_bar = false ;
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tic_id = tic() ;
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job_statuses = bqueue.run(maximum_wait_time, do_show_progress_bar) ;
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toc(tic_id)
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if all(job_statuses==1) ,
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fprintf('Done running landmark-matching.\n\n') ;
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else
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fprintf('Done running landmark-matching, but the job returned a non-zero error code.\n\n') ;
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end
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else
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% Useful for debugging
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landmark_match_all_tiles_in_z( ...
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raw_root_path, ...
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sample_memo_folder_path, ...
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landmark_root_path, ...
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z_point_match_root_path, ...
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do_force_computation) ;
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end

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