%SPEC load motor positions from spec

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% Source Code
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function p = spec(p)
import io.*
import utils.verbose
% make sure that spec data is available
if ~isfield(p.meta, 'spec')
    spec_aux = spec_read(p.specfile,'ScanNr',p.scan_number);
    if iscell(spec_aux)
        for ii=1:numel(p.scan_number)
            p.meta{ii}.spec = spec_aux{ii};
        end
    else
        p.meta{1}.spec = spec_aux;
    end
end


% check for continuous scans
for ii=1:numel(p.meta)
    outspec2 = p.meta{ii}.spec;
    if ~isempty(findstr(outspec2.S,'cont_line'))
        verbose(2, 'Continuous scan detected')
        p.scan.is_cont = true;
    end
end

% spec motor - can be defined in template
if isempty(p.spec.motor.fine_motors)
    verbose(2, 'Using default fine motor names: px, py')
    p.spec.motor.fine_motors{1} = 'py';
    p.spec.motor.fine_motors{2} = 'px';
end

% spec motor scaling - can be defined in template
if isempty(p.spec.motor.fine_motors_scale)
    p.spec.motor.fine_motors_scale = [1e-6 1e-6];
end

if numel(p.spec.motor.fine_motors) ~= numel(p.spec.motor.fine_motors_scale)
    error('Number of spec motors and scaling paramters does not match!')
end

for ii = 1:length(p.scan_number)
    
    if p.scan.is_cont % If its a continuous scan and spec coordinates were requested (checked above)
        % For cont_dmesh it needs defined coarse translations on template, piezo for slow axis and anything that
        % does not move for fast axis, e.g.   p.coarsex = 'samx'; p.coarsey
        % = 'py'
        % outspec2 = spec_read(p.specfile,'ScanNr',p.scan_number(ii));
        % Parse command
        remain = p.meta{ii}.spec.S;
        for k = 1:4;
            [fastmotor, remain] = strtok(remain);
        end
        [initrange, remain] = strtok(remain);
        [finalrange, remain] = strtok(remain);
        [numint, remain] = strtok(remain);
        verbose(2,['Cont_line in ' fastmotor ' from ' initrange ' to ' finalrange ' in ' numint ' intervals']);
        initrangedoub = str2double(initrange);
        finalrangedoub = str2double(finalrange);
        continterv = str2double(numint);
        contstep = (finalrangedoub-initrangedoub)/(continterv+2); % (+2) is a correction for effective smaller interval for continuous scans
        % Correction of range for average position in continuous scans
        initrangedoub = initrangedoub + contstep/2;
        finalrangedoub = finalrangedoub - contstep/2;
        contpos = 1e-3*linspace(initrangedoub,finalrangedoub,contstep+1).';
        % Note, in the above attempted to compensate for effective
        % smaller range in average position of probes in cont scans,
        % needs to be further tested
        if strcmp(fastmotor,'px')
            positions_real(:,2) = contpos;
            positions_real(:,1) = 0;
        elseif strcmp(fastmotor,'py')
            positions_real(:,1) = contpos;
            positions_real(:,2) = 0;
        end
        
    else
        % Use defined spec motors and scaling
        positions_real = [p.meta{ii}.spec.(p.spec.motor.fine_motors{1})*p.spec.motor.fine_motors_scale(1) p.meta{ii}.spec.(p.spec.motor.fine_motors{2})*p.spec.motor.fine_motors_scale(2)];

    end
    
    p.numpts(ii) = size(positions_real,1);
    p.positions_real = [p.positions_real ; positions_real]; 
end

end