Code covered by the BSD License  

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FRETSCAL

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FRETSCAL

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For the FRET analysis of images of yeast cells labeled with YFP and CFP.

fwriteline2cull( fjmp )
function fwriteline2cull( fjmp )
%Version 4/3/09 Writes the second line of the output files after culling,
%inspection and writes the params file for write final file.
global AOIshape CFPspill YFPspill primary intensitylimit bringthick bringincr separation
global YFPFWHMcull FRETFWHMcull CFPFWHMcull YFPmonocull FRETmonocull CFPmonocull YFPs2bcull FRETs2bcull CFPs2bcull
global YFPFWHM FRETFWHM CFPFWHM YFPmono FRETmono CFPmono YFPs2b FRETs2b CFPs2b
global maxmovement patchpixel bpfilter toobright context culled
global frettype yfptype cfptype limit1 limit2

if culled == 1  % the culling step was run
    if frettype == 1
        fprintf( fjmp, 'ExptType FRET ');
    end
    if yfptype == 1
        fprintf( fjmp, 'ExptType calcYFPspill ');
    end
    if cfptype == 1
        fprintf( fjmp, 'ExptType calcCFPspill ');
    end
    fprintf( fjmp, ' CFPspillfactor %6.3f',        CFPspill );
    fprintf( fjmp, ' YFPspillfactor %6.3f',        YFPspill );
    fprintf( fjmp, ' PrimaryChannel %d',        primary );
    fprintf( fjmp, ' YFPtargetFWHM %6.3f',  YFPFWHMcull );
    fprintf( fjmp, ' YFPtargetmono %6.3f',   YFPmonocull );
    fprintf( fjmp, ' YFPsignal2noise %6.3f', YFPs2bcull );
    fprintf( fjmp, ' FRETtargetFWHM %6.3f', FRETFWHMcull );
    fprintf( fjmp, ' FRETtargetmono %6.3f',  FRETmonocull );
    fprintf( fjmp, ' FRETsignal2noise %6.3f', FRETs2bcull );
    fprintf( fjmp, ' CFPtargetFWHM %6.3f',  CFPFWHMcull );
    fprintf( fjmp, ' CFPtargetmono %6.3f',   CFPmonocull );
    fprintf( fjmp, ' CFPsignal2noise %6.3f', CFPs2bcull );
    fprintf( fjmp, ' Bkg_incr %2d',      bringincr );
    fprintf( fjmp, ' Bkg_thick %2d',      bringthick );
    fprintf( fjmp, ' AOIshape %2d',           AOIshape );
    fprintf( fjmp, ' spotlimit %5.2f',        intensitylimit );
    fprintf( fjmp, ' separation %5.2f',     separation );
    fprintf( fjmp, ' context %5.2f',     context );
    fprintf( fjmp, ' toobright %5.2f',     toobright );
    fprintf( fjmp, ' bpfilter %d',    bpfilter );
    fprintf( fjmp, ' patchpixel %d',     patchpixel );
    fprintf(fjmp,  ' maxmovement %d',  maxmovement);
    fprintf(fjmp,  ' searchlimited %d', limit1);
    fprintf(fjmp,  ' culllimited %d\n', limit2);
else% culling step not run, so params  in output must reflect original search settings

    if frettype == 1
        fprintf( fjmp, 'ExptType FRET');
    end
    if yfptype == 1
        fprintf( fjmp, 'ExptType calcYFPspill');
    end
    if cfptype == 1
        fprintf( fjmp, 'ExptType calcCFPspill');
    end
    fprintf( fjmp, ' CFPspillfactor %6.3f',        CFPspill );
    fprintf( fjmp, ' YFPspillfactor %6.3f',        YFPspill );
    fprintf( fjmp, ' PrimaryChannel %d',        primary );
    fprintf( fjmp, ' YFPtargetFWHM %6.3f',  YFPFWHM );
    fprintf( fjmp, ' YFPtargetmono %6.3f',   YFPmono );
    fprintf( fjmp, ' YFPsignal2noise %6.3f', YFPs2b );
    fprintf( fjmp, ' FRETtargetFWHM %6.3f', FRETFWHM );
    fprintf( fjmp, ' FRETtargetmono %6.3f',  FRETmono );
    fprintf( fjmp, ' FRETsignal2noise %6.3f', FRETs2b );
    fprintf( fjmp, ' CFPtargetFWHM %6.3f',  CFPFWHM );
    fprintf( fjmp, ' CFPtargetmono %6.3f',   CFPmono );
    fprintf( fjmp, ' CFPsignal2noise %6.3f', CFPs2b );
    fprintf( fjmp, ' Bkg_incr %2d',      bringincr );
    fprintf( fjmp, ' Bkg_thick %2d',      bringthick );
    fprintf( fjmp, ' AOIshape %2d',           AOIshape );
    fprintf( fjmp, ' spotlimit %5.2f',        intensitylimit );
    fprintf( fjmp, ' separation %5.2f',     separation );
    fprintf( fjmp, ' context %5.2f',     context );
    fprintf( fjmp, ' toobright %5.2f',     toobright );
    fprintf( fjmp, ' bpfilter %d',    bpfilter );
    fprintf( fjmp, ' patchpixel %d',     patchpixel );
    fprintf(fjmp,  ' maxmovement %d',  maxmovement);
    fprintf(fjmp,  ' searchlimited %d', limit1);
    fprintf(fjmp,  ' culllimited %d\n', limit2);
end





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