gtSegmentationInitialise.m

function handles = gtSegmentationInitialise(handles)

% initialise handles structure for the segmentation GUI
% with acknowledgement of Peter's structure!

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% to display output at command line
set(handles.debug_checkbox, 'value', true)
handles.debug=true;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load parameters
load parameters
% add to the structure
handles.parameters = parameters;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if ~strcmp(handles.parameters.seg.method, 'doublethr_new')
handles.parameters.seg.method = 'doublethr_new';
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% how many images in this scan?
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(parameters.acq.type, '360degree')
    totproj = 2*parameters.acq.nproj;
elseif strcmp(parameters.acq.type, '180degree')
    totproj = parameters.acq.nproj;
else
    gtError('ACQ:invalid_parameter', ...
            'Unknown type of scan. Check parameters.acq.type!');
end
totproj = totproj-1;


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% populate the GUI with current parameters
% (option to reset to default parameters?)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% One quarter of detector, 10 images
set(handles.u_start, 'string', '1')
set(handles.u_end, 'string', num2str(round(parameters.detgeo.detsizeu/2)))
set(handles.v_start, 'string', '1')
set(handles.v_end, 'string', num2str(round(parameters.detgeo.detsizev/2)))
set(handles.image_start, 'string', num2str(round(totproj/2)))
set(handles.image_end, 'string', num2str(round(totproj/2)+9))
% start with the first image
handles.current_image = round(totproj/2);

% Subtract the background?
set(handles.subtract_median, 'value', parameters.seg.background_subtract)

% Seed thresholding parameters
set(handles.seed_thr, 'string', num2str(parameters.seg.thr_seed))
set(handles.seed_min_area, 'string', num2str(parameters.seg.seedminarea))

% Threshold hard limits
set(handles.thr_grow_low, 'string', num2str(parameters.seg.thr_grow_low))
set(handles.thr_grow_high, 'string', num2str(parameters.seg.thr_grow_high))

% Grow ratio, Min/Max size, extend increment
set(handles.thr_grow_ratio, 'string', num2str(parameters.seg.thr_grow_rat))
set(handles.min_blob_size, 'string', num2str(parameters.seg.minblobsize))
set(handles.max_blob_size, 'string', num2str(parameters.seg.maxblobsize))
set(handles.extend_blob_inc, 'string', num2str(parameters.seg.extendblobinc))

% Seg bounding box - start with the prep.bbox
handles.parameters.seg.bbox = parameters.prep.bbox;
handles.bb_handle = []; % a handle to the line drawn on the image

% OAR defaults
set(handles.OAR_walltime, 'string', '21600')
set(handles.OAR_njobs, 'string', parameters.oar.njobs)

% set status label to white
set(handles.status_label, 'BackgroundColor', 'w')
set(handles.status_label, 'string', 'Loading data...')


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Record if figures need to be updated
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% "global value" - something has changed
handles.values_changed = true;
% more specific details
handles.bb_changed = true; % re-threshold stacks
handles.thresholds_changed = true; % re-threshold stacks
handles.roi_changed = true; % reload stacks, then rethreshold