/usr/include/relion-1.3/src/ctffind_runner.h is in librelion-dev-common 1.3+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 | /***************************************************************************
*
* 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 CTFFIND_RUNNER_H_
#define CTFFIND_RUNNER_H_
#include <glob.h>
#include <vector>
#include <string>
#include <stdlib.h>
#include <stdio.h>
#include "src/metadata_table.h"
#include "src/image.h"
#include <src/time.h>
class CtffindRunner
{
public:
// I/O Parser
IOParser parser;
// Verbosity
int verb;
// Output rootname
FileName fn_in, fn_out;
// Filenames of all the micrographs to estimate the CTF from
std::vector<FileName> fn_micrographs;
// Dimension of squared area of the micrograph to use for CTF estimation
int ctf_win;
// CTFFIND3 executable
FileName fn_ctffind3_exe;
// Continue an old run: only estimate CTF if logfile WITH Final Values line does not yet exist, otherwise skip the micrograph
bool continue_old;
////// CTFFIND3 parameters
// Size of the box to calculate FFTw
double box_size;
// Minimum and maximum resolution (in A) to be taken into account
double resol_min, resol_max;
// Defocus search parameters (in A, positive is underfocus)
double min_defocus, max_defocus, step_defocus;
// Amount of astigmatism (in A)
double amount_astigmatism;
// Voltage (kV)
double Voltage;
// Spherical aberration
double Cs;
// Amplitude contrast (e.g. 0.07)
double AmplitudeConstrast;
// Magnification
double Magnification;
// Detector pixel size (um)
double PixelSize;
// Flag to only join results into a star file
bool do_only_join_results;
public:
// Read command line arguments
void read(int argc, char **argv, int rank = 0);
// Print usage instructions
void usage();
// Initialise some stuff after reading
void initialise();
// Execute all CTFFIND3 jobs to get CTF parameters
void run();
// Harvest all CTFFIND3 results into a single STAR file
void joinCtffindResults();
// Execute CTFFIND3 for a single micrograph
void executeCtffind3(FileName fn_mic);
};
// Get micrograph metadata
bool getCtffind3Results(FileName fn_mic, double &defU, double &defV, double &defAng, double &CC,
double &HT, double &CS, double &AmpCnst, double &XMAG, double &DStep, bool die_if_not_found = true);
#endif /* CTFFIND_RUNNER_H_ */
|