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vectorization_script_michael.m
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%% Michael's annular signal images
% SAM 8/14/2019
% signal_shape = 'annular' ;
signal_shape = 'spherical' ;
OutputDirectory = 'E:\Michael\' ;
PSF_fudge_factor = 1 ;
% start_workflow = 'energy' ;
% start_workflow = 'vertices' ;
% start_workflow = 'edges' ;
% start_workflow = 'network' ;
start_workflow = 'none' ;
switch start_workflow
case 'energy'
switch signal_shape
case 'annular'
input_image_name = 'tie2gfp16 9juyly2018 870nm region a-082-1.tif' ;
gaussian_to_ideal_ratio = 0.5 ;
spherical_to_annular_ratio = 0.5 ;
case 'spherical'
input_image_name = 'tie2gfp16 9juyly2018 870nm region a-082_Cycle00001_Ch3_00000.tif' ;
gaussian_to_ideal_ratio = 0.75 ;
spherical_to_annular_ratio = 0.5 ;
end
name_value_pair_inputs = { 'OutputDirectory', OutputDirectory, ...
'PreviousBatch', 'none', ...
'PreviousWorkflow', 'none', ...
'StartWorkflow', 'energy', ...
'FinalWorkflow', 'network', ...
'Visual', 'productive', ...
'NewBatch', 'yes', ...
'Presumptive', true, ...
... 'matching_kernel_string', '3D gaussian conv annular pulse', ...
'gaussian_to_ideal_ratio', gaussian_to_ideal_ratio, ...
... 'symmetry_ratio_factor', 0.1, ... !!!! depricated parameter
... 'symmetry_ratio_factor', 1/4, ...
'spherical_to_annular_ratio', spherical_to_annular_ratio, ...
'microns_per_voxel', 0.916*[1, 1, 2.18], ...
'radius_of_smallest_vessel_in_microns', 1.5, ...
'radius_of_largest_vessel_in_microns', 60, ...
'approximating_PSF', true, ...
'excitation_wavelength', 0.95 * PSF_fudge_factor, ...
'scales_per_octave', 6, ...
'max_voxels_per_node_energy', 1e6, ...
'vessel_wall_thickness_in_microns', 0 };
time_stamp = vectorize_V200([ OutputDirectory, input_image_name ], name_value_pair_inputs{ 1, : });
otherwise
name_value_pair_inputs = { 'OutputDirectory', OutputDirectory, ...
... 'PreviousBatch', 'recent', ...
'PreviousBatch', '190912-113508', ...
'PreviousWorkflow', 'recent', ...
'StartWorkflow', start_workflow, ...
... 'FinalWorkflow', 'network', ...
'Visual', 'productive', ...
'NewBatch', 'no', ...
'Presumptive', true, ...
'VertexCuration', 'none', ...
... 'EdgeCuration', 'manual' };
'EdgeCuration', 'none', ...
... 'SpecialOutput', { 'depth', 'strands', 'directions', 'upsampled', '3D-strands' }};
... 'SpecialOutput', { '3D-strands' }};
... 'SpecialOutput', { 'depth-stats' }};
'SpecialOutput', { 'depth', 'directions' }};
time_stamp = vectorize_V200( name_value_pair_inputs{ 1, : });
end