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replace_machine_edges_with_skeleton_points_2018_07_02.m
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replace_machine_edges_with_skeleton_points_2018_07_02.m
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close all
clear
sample_date = '2018-07-02' ;
this_file_path = mfilename('fullpath') ;
this_folder_path = fileparts(this_file_path) ;
%output_folder_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/cluster/%s/carver', sample_date) ;
output_folder_path = fullfile(this_folder_path, sprintf('%s-v02', sample_date)) ;
fragments_folder_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/cluster/Reconstructions/%s/prob0_swcs/frags', sample_date) ;
consensus_swcs_folder_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/shared_tracing/Finished_Neurons/%s', sample_date) ;
sample_folder_path = sprintf('/nrs/mouselight/SAMPLES/%s', sample_date) ;
skeleton_folder_path = sprintf('/groups/mousebrainmicro/mousebrainmicro/cluster/Reconstructions/%s/skeletonization', sample_date) ;
do_correct_fragments = true ;
% replace_machine_edges_with_skeleton_points(output_folder_path, ...
% fragments_folder_path, ...
% consensus_swcs_folder_path, ...
% sample_folder_path, ...
% skeleton_folder_path, ...
% do_correct_fragments) ;
% Get the metadata for the rendered sample
[shape_xyz, origin, spacing, jaws_origin] = load_sample_shape_origin_and_spacing(sample_folder_path);
% Load the fragments from disk
all_uncorrected_fragment_xyzs_in_erhan_coords = ...
compute_or_read_from_memo(output_folder_path, ...
'all_uncorrected_fragment_xyzs_in_erhan_coords', ...
@()(read_all_fragment_centerpoints(fragments_folder_path))) ;
% Check that the fragment nodes are on the grid as we expect
% all_fragment_ijks_unrounded = (all_fragment_xyzs_in_erhan_coords - origin) ./ spacing + 0.5 ; % these should be one-based ijks
% all_fragment_ijks = round(all_fragment_ijks_unrounded) ; % these should be one-based ijks
% fragment_offsets = all_fragment_ijks_unrounded - all_fragment_ijks ;
% assert( all( all( abs(fragment_offsets) < spacing/1024 ) ) ) ; % the offsets should just be floating-point error
fraction_of_uncorrected_fragment_nodes_at_voxel_centers = ...
fraction_of_xyzs_at_voxel_centers_using_erhan_conventions(all_uncorrected_fragment_xyzs_in_erhan_coords, spacing, origin)
assert( fraction_of_uncorrected_fragment_nodes_at_voxel_centers == 1) ;
% Convert fragment coords to JaWS coords
all_uncorrected_fragment_ijks_unrounded = (all_uncorrected_fragment_xyzs_in_erhan_coords - origin) ./ spacing + 0.5 ; % these should be one-based ijks
all_uncorrected_fragment_ijks = round(all_uncorrected_fragment_ijks_unrounded) ; % these should be one-based ijks
% Get the skeleton graph, either from .txt files or from mat
graph_file_path = fullfile(output_folder_path, 'skeleton-as-graph.mat') ;
if exist(graph_file_path, 'file') ,
load(graph_file_path, 'skeleton_graph', 'skeleton_ijks') ;
else
[skeleton_graph, skeleton_ijks] = load_skeleton_graph_from_txt_files(skeleton_folder_path, shape_xyz) ; % these ijks are also one-based
save(graph_file_path, 'skeleton_graph','skeleton_ijks', '-v7.3') ;
end
% What fraction of uncorrected fragment points are also skeleton points
is_uncorrected_fragment_a_skeleton_point = is_point_drawn_from_pool(all_uncorrected_fragment_ijks, skeleton_ijks, spacing) ;
fraction_uncorrected_fragment_points_that_are_skeleton_points = mean(is_uncorrected_fragment_a_skeleton_point)
% Correct the fragment ijks, if requested
if do_correct_fragments ,
all_fragment_ijks = all_uncorrected_fragment_ijks + 1 ;
else
all_fragment_ijks = all_uncorrected_fragment_ijks ;
end
% What fraction of corrected fragment points are also skeleton points
is_fragment_a_skeleton_point = is_point_drawn_from_pool(all_fragment_ijks, skeleton_ijks, spacing) ;
fraction_fragment_points_that_are_skeleton_points = mean(is_fragment_a_skeleton_point)
assert( fraction_of_uncorrected_fragment_nodes_at_voxel_centers > 0.5) ;
% Convert one-based voxel indices to voxel center coords in JaWS coord system
all_uncorrected_fragment_xyzs = jaws_origin + spacing .* (all_uncorrected_fragment_ijks-1) ; % um, n x 3
all_fragment_xyzs = jaws_origin + spacing .* (all_fragment_ijks-1) ; % um, n x 3
skeleton_xyzs = jaws_origin + spacing .* (skeleton_ijks-1) ; % um, n x 3
% skeleton_ijks are 1-based, we want to map them to voxel centers
% in JaWS coordinates
% % Write the skeleton to json file, for Will & Jan
% graph_as_json_file_path = fullfile(output_folder_path, 'skeleton-as-graph.json') ;
% if ~exist(graph_as_json_file_path, 'file') ,
% json_ready_skeleton = struct() ;
% json_ready_skeleton.ijks = skeleton_ijks-1 ; % convert to zero-based indexing
% edges_with_third_col = table2array(skeleton_graph.Edges)-1 ; % convert to zero-based indexing
% json_ready_skeleton.edges = edges_with_third_col(:,1:2) ;
% json_ready_skeleton.jaws_origin = jaws_origin ;
% json_ready_skeleton.spacing = spacing ;
% json_ready_skeleton.origin = origin ;
% json_ready_skeleton.shape_xyz = shape_xyz ;
% json_ready_skeleton.xyz_from_ijk_formula = 'xyzs = jaws_origin + spacing .* ijks' ;
% json_text = jsonencode(json_ready_skeleton) ;
% dump_string_to_file(graph_as_json_file_path, json_text) ;
% end
% Load in the consensus neurons
consensus_neurons_and_names = compute_or_read_from_memo(output_folder_path, ...
'consensus_neurons', ...
@()(collect_consensus_neurons(consensus_swcs_folder_path))) ;
consensus_neurons = consensus_neurons_and_names.consensus_neurons ;
consensus_neuron_names = consensus_neurons_and_names.consensus_neuron_names ;
% Check that those neurons are on-grid
% This currently fails for 2018-07-02 consensus neurons. It's true
% that the vast majority of the nodes are on-grid, but some are not.
% Should investigate at some point
consensus_neuron_xyzs = xyzs_from_neuron_structs(consensus_neurons) ;
% assert( are_all_xyzs_at_voxel_centers(consensus_neuron_xyzs, spacing, jaws_origin) ) ;
fraction_of_consensus_nodes_at_voxel_centers = fraction_of_xyzs_at_voxel_centers_using_jaws_conventions(consensus_neuron_xyzs, spacing, jaws_origin)
%assert( fraction_of_consensus_nodes_at_voxel_centers == 1) ;
% What fraction of the consensus nodes are fragment nodes for the uncorrected
% fragments
is_consensus_node_an_uncorrected_fragment_node = is_point_drawn_from_pool(consensus_neuron_xyzs, all_uncorrected_fragment_xyzs, spacing) ;
fraction_of_consensus_nodes_that_are_uncorrected_fragment_nodes = mean(is_consensus_node_an_uncorrected_fragment_node)
% What fraction of the consensus nodes are fragment nodes
is_consensus_node_a_fragment_node = is_point_drawn_from_pool(consensus_neuron_xyzs, all_fragment_xyzs, spacing) ;
fraction_of_consensus_nodes_that_are_fragment_nodes = mean(is_consensus_node_a_fragment_node)
%%
% Label the consensus neuron nodes as being machine-generated or not
consensus_neurons_with_machine_centerpoints_labelled = ...
compute_or_read_from_memo(output_folder_path, ...
'consensus_neurons_with_machine_centerpoints_labelled', ...
@()(label_machine_centerpoints_in_neurons(consensus_neurons, consensus_neuron_names, all_fragment_xyzs, spacing))) ;
%%
% Splice in skeleton nodes where possible
consensus_neurons_augmented_with_skeleton_nodes = ...
compute_or_read_from_memo(output_folder_path, ...
'consensus_neurons_augmented_with_skeleton_nodes', ...
@()(replace_machine_edges_with_skeleton_points_in_neurons(consensus_neurons_with_machine_centerpoints_labelled, ...
consensus_neuron_names, ...
skeleton_graph, ...
skeleton_xyzs, ...
spacing))) ;
%%
% Write the swc's that don't exist already
consensus_neuron_count = length(consensus_neurons) ;
swc_folder_path = fullfile(output_folder_path, 'augmented-with-skeleton-nodes-as-swcs') ;
if consensus_neuron_count>0 && ~exist(swc_folder_path, 'file') ,
mkdir(swc_folder_path) ;
end
for i = 1:consensus_neuron_count ,
consensus_neuron_name = consensus_neuron_names{i} ;
swc_file_name = sprintf('%s.swc', consensus_neuron_name) ;
swc_file_path = fullfile(swc_folder_path, swc_file_name) ;
if ~exist(swc_file_path, 'file') ,
save_swc(swc_file_path, consensus_neurons_augmented_with_skeleton_nodes{i}, consensus_neuron_name) ;
end
end