3fc7712f3cf5329220e75d5dd75d8a1ad0d24be1,cellprofiler/modules/correctilluminationcalculate.py,CorrectIlluminationCalculate,create_settings,#CorrectIlluminationCalculate#,79

Before Change

                                            <i>(Used only if the dilated image is to be retained for later use in the pipeline)</i><br>
                                            Enter a name that will allow the dilated image to be selected later in the pipeline.""")
        
        self.automatic_splines = cps.Binary(
            "Automatically calculate spline parameters?", True,
            doc = 
            <i>(Used only if Splines are selected for the smoothing method)</i><br>
            Leave this setting checked to automatically calculate
            the parameters for spline fitting. Uncheck the setting to
            specify the background mode, background threshold, scale,
            maximum // of iterations and convergence.)
        
        self.spline_bg_mode = cps.Choice(
            "Background mode",
            [MODE_AUTO, MODE_DARK, MODE_BRIGHT, MODE_GRAY],

After Change

        
        self.rescale_option = cps.Choice(
            "Rescale the illumination function?",
            [cps.YES, cps.NO, RE_MEDIAN], doc = """
            The illumination function can be rescaled so that the pixel intensities
            are all equal to or greater than 1. You have the following options:
            <ul>
            <li><i>Yes:</i> Rescaling is recommended if you plan to
            use the <i>Regular</i> method (and hence, the <i>Division</i> option in 
            <b>CorrectIlluminationApply</b>) so that the corrected images are in the 
            range 0 to 1.</li>
            <li><i>No:</i> Rescaling is not recommended if you plan to use the <i>Background</i> 
            method, which is paired with the <i>Subtract</i> option in <b>CorrectIlluminationApply</b>. 
            Note that as a result of the illumination function being rescaled from 1 to
            infinity, the rescaling of each image might be dramatic if there is substantial 
            variation across the field of view, causing the corrected images
            to be very dark. </li>
            <li>%(RE_MEDIAN)s<i>:</i> This option chooses the median value in the 
            image to rescale so that division increases some values and decreases others.</li>
            </ul>"""%globals())
        
        self.each_or_all = cps.Choice(
            "Calculate function for each image individually, or based on all images?",

Instances