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@mihelics
mihelics authored May 11, 2022
1 parent 8ef76b8 commit d0385a1
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Showing 4 changed files with 27 additions and 20 deletions.
8 changes: 4 additions & 4 deletions source/combine_strands.m
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Expand Up @@ -76,13 +76,13 @@ function combine_strands( path_to_energy_settings, path_to_energy_data, path_to_
- x( 1 : end - 1, 1 : 3 )), [ ], 'all' ), ...
strand_subscripts );

if any( strand_max_delta_length > 1 + exp( -15 ))
if any( strand_max_delta_length > 2)

warning('discontinuity in strand')

strand_subscripts{strand_max_delta_length > 1 + exp( -15 )}
strand_max_delta_length(strand_max_delta_length > 1 + exp( -15 ))
find(strand_max_delta_length > 1 + exp( -15 ))
strand_subscripts{strand_max_delta_length > 2}
strand_max_delta_length(strand_max_delta_length > 2)
find(strand_max_delta_length > 2)

end

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4 changes: 2 additions & 2 deletions source/get_edges_V300.m
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Expand Up @@ -101,8 +101,8 @@
% edge_number_tolerance = 3 ; % number of edges per vertex SAM 10/29/21 17:55 % SAM 12/24/21
% second_max_edges_per_vertex = max_edges_per_vertex ;
% radius_tolerance = 0.0801 ; % fractional change of radius from origin vertex radius
radius_tolerance = 0.2 ; % fractional change of radius from origin vertex radius % SAM 4/12/21
% radius_tolerance = 0.5 ; % fractional change of radius from origin vertex radius % SAM 10/27/21
% radius_tolerance = 0.2 ; % fractional change of radius from origin vertex radius % SAM 4/12/22
radius_tolerance = 0.5 ; % fractional change of radius from origin vertex radius % SAM 10/27/21
% radius_tolerance = 1 ; % SAM 12/24/21
% radius_tolerance = 1.5 ; % SAM 1/11/22
% radius_tolerance = 2/3 ; % 11/7/21 % SAM 1/21/22
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15 changes: 10 additions & 5 deletions source/noise_sensitivity_study_V2.m
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Expand Up @@ -113,17 +113,22 @@
% % % energy_time_stamp = batch_time_stamp ;
% % % network_time_stamp = '220205-030821' ;
%
% output_directory = 'E:\Blinder\' ;
% batch_time_stamp = '220207-133605' ;
% energy_time_stamp = batch_time_stamp ;
% network_time_stamp = '220207-150624' ;
% % output_directory = 'E:\Blinder\' ;
% % batch_time_stamp = '220207-133605' ;
% % energy_time_stamp = batch_time_stamp ;
% % network_time_stamp = '220207-150624' ;
%
% % % SAM 1/5/22
% % output_directory = 'E:\Annie\120827 Alankrit\hr_mf\' ;
% % batch_time_stamp = '220104-234034' ;
% % energy_time_stamp = batch_time_stamp ;
% % network_time_stamp = batch_time_stamp ;
%
% % SAM 5/5/22
% output_directory = 'E:\2P imaging\2021_Chronic_Imaging\Doug week 1\' ;
% batch_time_stamp = '220126-010215' ;
% energy_time_stamp = batch_time_stamp ;
% network_time_stamp = '220505-042233' ;
%
% [ batch_directory, visual_data_directory, visual_vector_directory, vector_directory, settings_directory ] = get_directories( output_directory, batch_time_stamp );
%
Expand Down Expand Up @@ -805,7 +810,7 @@
if is_testing_machine_curation, if is_using_same_vertex_set, k_index_range = k_index_range_temp ; time_stamps_edges{ 2 } = time_stamps_edges{ 1 }; end, end

is_first_time_running_vertices = false ;
% %% Compare classification strength of rendered, weighted edges and of the observed intensity
%% Compare classification strength of rendered, weighted edges and of the observed intensity

% number_of_thresholds = 101 ;

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20 changes: 11 additions & 9 deletions source/vectorization_script_Shaun.m
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Expand Up @@ -37,11 +37,12 @@

% input_names{ 1 } = 'Eddy_Fused_Raw_w3.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Eddy week 3\' ; % SAM 6/16/21
% input_names{ 1 } = 'Eddy_Fused_Raw_w5.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Eddy week 5\' ; % SAM 6/18/21
input_names{ 1 } = 'Doug_Fused_Raw_w1.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Doug week 1\' ; % SAM 6/26/21 %% SAM 3/17/22
% input_names{ 1 } = 'Doug_Fused_Raw_w1.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Doug week 1\' ; % SAM 6/26/21 %% SAM 3/17/22
% input_names{ 1 } = 'Dan_w1_01.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Dan week 1\' ; % SAM 8/6/21 SAM
% input_names{ 2 } = 'Dan_w1_02.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Dan week 1\' ; % SAM 8/10/21 SAM
% for idx = 3 : 6, input_names{ idx - 2 } = [ 'Dan_w1_0', num2str(idx), '.tif' ]; end, OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Dan week 1\' ; % SAM 8/10/21 SAM
% input_names{ 1 } = 'Dan_Fused_Raw_w1.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Dan week 1\fused\' ; % SAM 9/2/21
input_names{ 1 } = 'Elmer_Fused_Raw_w1.tif' ; OutputDirectory = 'E:\2P imaging\2021_Chronic_Imaging\Elmer week 1\' ; % SAM 6/26/21 %% SAM 3/17/22

microns_per_voxel = [ ];
% microns_per_voxel( 1, 1 : 3 ) = [1.34, 1.36, 3]; % [ y, x, z ] == microns_per_voxel - SAM 3/19/21
Expand All @@ -56,8 +57,8 @@
% start_workflow = 'energy' ;
% start_workflow = 'vertices' ;
% start_workflow = 'edges' ;
% start_workflow = 'network' ;
start_workflow = 'none' ;
start_workflow = 'network' ;
% start_workflow = 'none' ;

% Settings:

Expand Down Expand Up @@ -113,24 +114,25 @@
... 'Visual', 'vertices', ...
'NewBatch', 'no', ...
'Presumptive', true, ...
... 'VertexCuration', 'manual', ...
... 'VertexCuration', 'manual', ...
... 'VertexCuration', 'none', ...
... 'VertexCuration', 'mutual edges', ...
... 'VertexCuration', 'auto', ...
'space_strel_apothem_edges', int64(1), ...
'number_of_edges_per_vertex', 2, ...
... 'number_of_edges_per_vertex', 4, ...
'sigma_edge_smoothing', 0.5, ...
... 'EdgeCuration', 'manual', ...
... 'EdgeCuration', 'manual', ...
... 'EdgeCuration', 'none', ...
... 'SpecialOutput', { 'depth', 'strands', 'directions', 'upsampled', '3D-strands' }};
... 'SpecialOutput', { '3D-strands' }};
... 'SpecialOutput', { 'depth-stats' }};
... 'SpecialOutput', { 'upsampled' }};
... 'is_combining_strands', false,'SpecialOutput', { 'upsampled' }};
... 'SpecialOutput', { 'depth', 'directions' }};
... 'SpecialOutput', { 'histograms', 'vmv', 'depth', 'strands', 'directions' }};
... 'SpecialOutput', 'flow-field' };
'SpecialOutput', {'histograms'}};
... 'is_combining_strands', false,'SpecialOutput', { 'histograms', 'vmv', 'depth', 'strands', 'directions' }};
'is_combining_strands', true, 'SpecialOutput', { 'histograms', 'flow-field' }};
... 'SpecialOutput', {'histograms'}};
... 'SpecialOutput', { 'vmv', 'directions' }};

time_stamp = vectorize_V200( name_value_pair_inputs{ 1, : });
end
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