void defineParams()
    {

        addUsageLine("Align two volumes varying orientation, position and scale");
        addParamsLine("   --i1 <volume1>        : the first volume to align");
        addParamsLine("   --i2 <volume2>        : the second one");
        addParamsLine("  [--rot   <rot0=0>  <rotF=0>  <step_rot=1>]  : in degrees");
        addParamsLine("  [--tilt  <tilt0=0> <tiltF=0> <step_tilt=1>] : in degrees");
        addParamsLine("  [--psi   <psi0=0>  <psiF=0>  <step_psi=1>]  : in degrees");
        addParamsLine("  [--scale <sc0=1>   <scF=1>   <step_sc=1>]   : size scale margin");
        addParamsLine("  [--grey_scale <sc0=1> <scF=1> <step_sc=1>]  : grey scale margin");
        addParamsLine("    requires --least_squares;");
        addParamsLine("  [--grey_shift <sh0=0> <shF=0> <step_sh=1>]  : grey shift margin");
        addParamsLine("    requires --least_squares;");
        addParamsLine("  [-z <z0=0> <zF=0> <step_z=1>] : Z position in pixels");
        addParamsLine("  [-y <y0=0> <yF=0> <step_y=1>] : Y position in pixels");
        addParamsLine("  [-x <x0=0> <xF=0> <step_x=1>] : X position in pixels");
        addParamsLine("  [--show_fit]      : Show fitness values");
        addParamsLine("  [--apply <file=\"\">] : Apply best movement to --i2 and store results in this file");
        addParamsLine("  [--covariance]    : Covariance fitness criterion");
        addParamsLine("  [--least_squares] : LS fitness criterion");
        addParamsLine("  [--local]         : Use local optimizer instead of exhaustive search");
        addParamsLine("  [--frm <maxFreq=0.25> <maxShift=10>] : Use Fast Rotational Matching");
        addParamsLine("                    : Maximum frequency is in digital frequencies (<0.5)");
        addParamsLine("                    : Maximum shift is in pixels");
        addParamsLine("                    :+ See Y. Chen, et al. Fast and accurate reference-free alignment of subtomograms. JSB, 182: 235-245 (2013)");
        addParamsLine("  [--onlyShift]     : Only shift");
        addParamsLine(" == Mask Options == ");
        mask.defineParams(this,INT_MASK,NULL,NULL,true);
        addExampleLine("Typically you first look for a rough approximation of the alignment using exhaustive search. For instance, for a global rotational alignment use",false);
        addExampleLine("xmipp_volume_align --i1 volume1.vol --i2 volume2.vol --rot 0 360 15 --tilt 0 180 15 --psi 0 360 15");
        addExampleLine("Then, assume the best alignment is obtained for rot=45, tilt=60, psi=90",false);
        addExampleLine("Now you perform a local search to refine the estimation and apply",false);
        addExampleLine("xmipp_volume_align --i1 volume1.vol --i2 volume2.vol --rot 45 --tilt 60 --psi 90 --local --apply volume2aligned.vol");
    }
Example #2
0
 // Define parameters
 void defineParams()
 {
     each_image_produces_an_output = true;
     XmippMetadataProgram::defineParams();
     addUsageLine("Finds the 3D center of mass and center the volume around this point");
     mask_prm.defineParams(this,INT_MASK,NULL,"Restrict the center of mass to the mask area.");
     addExampleLine("xmipp_volume_center -i volume.vol -o volumeCentered.vol");
 }
    void defineParams()
    {
        each_image_produces_an_output = true;

        addUsageLine("Adjust the grey level value of the pixels to a specified range.");
        addKeywords("mask, normalization");
        addSeeAlsoLine("transform_normalize");
        XmippMetadataProgram::defineParams();
        addParamsLine("   --range <min_val> <max_val> : Output minimum and maximum values.");
        addParamsLine("   alias -r;");
        addParamsLine("   [--noise <sigma=0>] : Variation of the limit range values.");
        mask_prm.defineParams(this,INT_MASK, NULL, "Pixels in the mask area are guaranteed to be into the specified range.");

        addExampleLine("Adjust an image in the range [-1, 1]:", false);
        addExampleLine("xmipp_transform_range_adjust -i image.xmp -o image_adjust.xmp --range -1 1");
        addExampleLine("Adjust images in a stack applying a circular mask:", false);
        addExampleLine("xmipp_transform_range_adjust -i images.stk -o image_adjust.stk --range -1 1 --mask circular -32");
        addExampleLine("Adjust a selection file in the range [-100, 100] with sigma noise 10:", false);
        addExampleLine("xmipp_transform_range_adjust -i selection.sel --oroot images/im_adjust:spi -o selection_adjust.sel --range -100 100 --noise 10");
    }