dp_node_dmri_topup_prep.m

classdef dp_node_dmri_topup_prep < dp_node

    % pulls out data and saves it in ap pa order

    methods

        function obj = dp_node_dmri_topup_prep()

            obj.input_test = {...
                'nii_ap_fn', 'nii_pa_fn', ...
                'xps_ap_fn', 'xps_pa_fn'};

        end

        % dp_node_dmri_topup_io has been executed before this
        % ensuring the presence of nii_ap_fn and nii_pa_fn
        function input = po2i(~, po)
            input = po;
            input = msf_ensure_field(input, 'xps_ap_fn', mdm_xps_fn_from_nii_fn(po.nii_ap_fn));
            input = msf_ensure_field(input, 'xps_pa_fn', mdm_xps_fn_from_nii_fn(po.nii_pa_fn));
        end

        function output = i2o(obj, input)

            % Pass on input to next node
            output = input;

            output.topup_nii_fn = fullfile(output.op, 'topupinput.nii.gz');
            output.topup_spec_fn = fullfile(output.op, 'topup.txt');
            output.topup_xps_fn = mdm_xps_fn_from_nii_fn(output.topup_nii_fn);

            % add a temporary path
            output.tmp.bp = msf_tmp_path();
            output.tmp.do_delete = 1;
            

        end

        function output = execute(obj, input, output)

            % define options
            opt = mdm_opt();

            % connect to data
            s_ap = mdm_s_from_nii(input.nii_ap_fn);
            s_pa = mdm_s_from_nii(input.nii_pa_fn);

            % define temporary working path, create output dir
            wp = output.tmp.bp;
            msf_mkdir(output.op);

            % Pull out the b0 / low b0 volumes
            s_pa_b0 = mdm_s_subsample(s_pa, s_pa.xps.b <= 0.11e9, wp, opt);
            s_ap_b0 = mdm_s_subsample(s_ap, s_ap.xps.b <= 0.11e9, wp, opt);

            % Prepare powder average and merge (average all)
            s_pa_b0.xps.a_ind = s_pa_b0.xps.b >= 0;
            s_ap_b0.xps.a_ind = s_ap_b0.xps.b >= 0;

            s_pa_b0.xps = msf_rmfield(s_pa_b0.xps, 's_ind');
            s_ap_b0.xps = msf_rmfield(s_ap_b0.xps, 's_ind');

            % Powder average and merge
            s_pa_b0 = mdm_s_powder_average(s_pa_b0, wp, opt);
            s_ap_b0 = mdm_s_powder_average(s_ap_b0, wp, opt);
            s = mdm_s_merge({s_ap_b0, s_pa_b0}, wp, 'topup', opt);

            % Copy file
            copyfile(s.nii_fn, output.topup_nii_fn);
            mdm_xps_save(s.xps, output.topup_xps_fn);

            % Write topup specification file
            % xxx: this should find correct information from a json file
            mdm_txt_write({'0 1 0 0.1', '0 -1 0 0.1'}, ...
                output.topup_spec_fn, opt);

        end
    end
end