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Folded in http://github.com/MouseLightProject/freezing repo as of commit 6f0a07bc, dated 2023-05-24
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‎.gitignore

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foreground-classifiers/data/
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foreground-classifiers/2021-03-17/
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RESTORED/
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freezing/octree*test*folder
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freezing/raw-tiles*test*folder
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‎freezing/are_files_same_size_and_md5sum.m

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function result = are_files_same_size_and_md5sum(file_name_1, file_name_2)
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file_size_1 = get_file_size(file_name_1) ;
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file_size_2 = get_file_size(file_name_2) ;
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if file_size_1 ~= file_size_2 ,
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result = false ;
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return
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end
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result = are_md5s_the_same(file_name_1, file_name_2) ;
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end

‎freezing/batch_convert_all_mj2_files_to_tif.m

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function batch_convert_all_mj2_files_to_tif(output_folder_name, ...
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input_folder_name, ...
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do_submit, ...
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do_try, ...
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maximum_running_slot_count, ...
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submit_host_name)
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% Find all .mj2 files in folders with no subfolders, convert them to .tif
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slots_per_job = 1 ;
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bsub_options = '-P mouselight -W 59 -J thaw' ;
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find_and_batch(input_folder_name, ...
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@is_a_mj2_and_target_missing, ...
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@tif_from_mj2_single_for_find_and_batch, ...
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'do_submit', do_submit, ...
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'do_try', do_try, ...
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'submit_host_name', submit_host_name, ...
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'maximum_running_slot_count', maximum_running_slot_count, ...
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'slots_per_job', slots_per_job, ...
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'bsub_options', bsub_options, ...
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'predicate_extra_args', {input_folder_name, output_folder_name}, ...
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'batch_function_extra_args', {input_folder_name, output_folder_name}) ;
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end

‎freezing/batch_convert_all_tif_files_to_mj2.m

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function batch_convert_all_tif_files_to_mj2(mj2_folder_name, ...
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tif_folder_name, ...
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compression_ratio, ...
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do_submit, ...
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do_try, ...
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maximum_running_slot_count, ...
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submit_host_name)
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% Find all .tif files in folder tree, convert them to .mj2
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slots_per_job = 1 ;
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bsub_options = '-P mouselight -W 59 -J freeze' ;
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find_and_batch(tif_folder_name, ...
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@does_file_name_end_in_dot_tif_and_mj2_is_missing, ...
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@mj2_from_tif_single_for_find_and_batch, ...
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'do_submit', do_submit, ...
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'do_try', do_try, ...
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'submit_host_name', submit_host_name, ...
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'maximum_running_slot_count', maximum_running_slot_count, ...
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'slots_per_job', slots_per_job, ...
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'bsub_options', bsub_options, ...
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'predicate_extra_args', {tif_folder_name, mj2_folder_name}, ...
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'batch_function_extra_args', {tif_folder_name, mj2_folder_name, compression_ratio}) ;
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end

‎freezing/batch_verify_mj2_files_after_freezing.m

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function batch_preverify_stack_files_after_freezing(mj2_folder_name, ...
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tif_folder_name, ...
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do_submit, ...
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do_try, ...
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submit_host_name, ...
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maximum_running_slot_count)
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% Makes sure all the big target files are present in the the destination, and
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% are similar to their source files.
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slots_per_job = 4 ;
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bsub_options = '-P mouselight -W 59 -J verify-frozen' ;
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find_and_batch(tif_folder_name, ...
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@does_need_preverification_after_freezing, ...
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@verify_single_mj2_file_after_freezing, ...
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'do_submit', do_submit, ...
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'do_try', do_try, ...
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'submit_host_name', submit_host_name, ...
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'maximum_running_slot_count', maximum_running_slot_count, ...
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'slots_per_job', slots_per_job, ...
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'bsub_options', bsub_options, ...
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'predicate_extra_args', {tif_folder_name, mj2_folder_name}, ...
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'batch_function_extra_args', {tif_folder_name, mj2_folder_name}) ;
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end

‎freezing/batch_verify_tif_files_after_thawing.m

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function batch_verify_tif_files_after_thawing(output_folder_name, ...
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input_folder_name, ...
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do_submit, ...
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do_try, ...
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submit_host_name, ...
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maximum_running_slot_count)
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% Makes sure all the leaf image files are present in the the destination, and
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% are similar to their source files.
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slots_per_job = 4 ;
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bsub_options = '-P mouselight -W 59 -J verify-thawed-stack' ;
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find_and_batch(input_folder_name, ...
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@is_mj2_and_lacks_cert_for_output, ...
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@verify_single_tif_file_after_thawing, ...
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'do_submit', do_submit, ...
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'do_try', do_try, ...
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'submit_host_name', submit_host_name, ...
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'maximum_running_slot_count', maximum_running_slot_count, ...
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'slots_per_job', slots_per_job, ...
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'bsub_options', bsub_options, ...
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'predicate_extra_args', {input_folder_name, output_folder_name}, ...
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'batch_function_extra_args', {input_folder_name, output_folder_name}) ;
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end

‎freezing/check_certs_after_verifying_freezing.m

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function check_certs_after_verifying_freezing(tif_root_folder_path, mj2_root_folder_path)
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% Makes sure there's a .similar-mj2-exists for each .tif file in
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% tif_root_folder_path.
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function result = verify_single_tif_file_after_mj2_from_tif_wrapper(tif_root_folder_path, tif_folder_relative_path, tif_file_name, depth) %#ok<INUSD>
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result = verify_single_tif_file_after_mj2_from_tif(tif_root_folder_path, tif_folder_relative_path, tif_file_name, mj2_root_folder_path) ;
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end
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find_and_verify(...
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tif_root_folder_path, ...
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@does_file_name_end_in_dot_tif, ...
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@verify_single_tif_file_after_mj2_from_tif_wrapper, ...
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@is_not_the_ktx_folder) ;
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end

‎freezing/check_certs_after_verifying_thawing.m

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function check_certs_after_verifying_thawing(input_root_folder_path, output_root_folder_path)
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% Makes sure there's a .similar-tif-exists for each .mj2 file in
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% input_root_folder_path.
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function result = check_single_cert_after_verifying_thawing_wrapper(root_folder_path, base_folder_relative_path, file_name, depth) %#ok<INUSD>
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result = check_single_cert_after_verifying_thawing(root_folder_path, base_folder_relative_path, file_name, output_root_folder_path) ;
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end
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find_and_verify(...
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input_root_folder_path, ...
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@does_file_name_end_in_dot_mj2, ...
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@check_single_cert_after_verifying_thawing_wrapper, ...
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@(varargin)(true)) ;
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end

‎freezing/check_single_cert_after_verifying_thawing.m

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function result = check_single_cert_after_verifying_thawing(...
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input_root_folder_path, input_folder_relative_path, input_file_name, output_root_folder_path) %#ok<INUSD>
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output_file_name = replace_extension(input_file_name, '.tif') ;
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output_file_path = fullfile(output_root_folder_path, input_folder_relative_path, output_file_name) ;
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cert_file_path = horzcat(output_file_path, '.is-similar-to-mj2') ;
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result = logical( exist(cert_file_path, 'file') ) ;
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end

‎freezing/copy_file_for_find_and_batch.m

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function copy_file_for_find_and_batch(tif_side_file_path, tif_root_folder_name, mj2_root_folder_name, varargin)
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relative_file_path_of_tif_side_file = relpath(tif_side_file_path, tif_root_folder_name) ;
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relative_file_path_of_mj2_side_file = relative_file_path_of_tif_side_file ;
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mj2_side_file_path = fullfile(mj2_root_folder_name, relative_file_path_of_mj2_side_file) ;
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mj2_side_folder_path = fileparts2(mj2_side_file_path) ;
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ensure_folder_exists(mj2_side_folder_path) ;
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copyfile(tif_side_file_path, mj2_side_file_path) ;
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end

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