/usr/include/relion-1.4/src/mask.h is in librelion-dev-common 1.4+dfsg-1build1.
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*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
#ifndef MASK_H_
#define MASK_H_
#include "src/multidim_array.h"
#include "src/fftw.h"
#include "src/time.h"
// Mask out corners outside sphere (replace by average value)
// Apply a soft mask (raised cosine with cosine_width pixels width)
void softMaskOutsideMap(MultidimArray<DOUBLE> &vol, DOUBLE radius = -1., DOUBLE cosine_width = 3, MultidimArray<DOUBLE> *Mnoise = NULL);
// Apply a soft mask and set density outside the mask at the average value of those pixels in the original map
void softMaskOutsideMap(MultidimArray<DOUBLE> &vol, MultidimArray<DOUBLE> &msk, bool invert_mask = false);
// Make an automated mask, based on:
// 1. initial binarization (based on ini_mask_density_threshold)
// 2. Growing extend_ini_mask in all directions
// 3. Putting a raised-cosine edge on the mask with width width_soft_mask_edge
// If verb, then output description of steps and progress bars
void autoMask(MultidimArray<DOUBLE> &img_in, MultidimArray<DOUBLE> &msk_out,
DOUBLE ini_mask_density_threshold, DOUBLE extend_ini_mask, DOUBLE width_soft_mask_edge, bool verb = false);
// Fills mask with a soft-edge circular mask (soft-edge in between radius and radius_p), centred at (x, y, z)
void raisedCosineMask(MultidimArray<DOUBLE> &mask, DOUBLE radius, DOUBLE radius_p, int x, int y, int z = 0);
#endif /* MASK_H_ */
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