<commit_before>/* Copyright 2013. The Regents of the University of California.
 * Copyright 2015-2016. <NAME>.
 * All rights reserved. Use of this source code is governed by
 * a BSD-style license which can be found in the LICENSE file.
 *
 * Authors: 
 * 2012-2016 <NAME> <<EMAIL>>
 */

#include <stdbool.h>
#include <complex.h>
#include <math.h>

#include "num/multind.h"
#include "num/flpmath.h"
#include "num/fft.h"
#include "num/init.h"

#include "misc/mri.h"
#include "misc/misc.h"
#include "misc/mmio.h"
#include "misc/utils.h"
#include "misc/opts.h"
#include "misc/debug.h"

#include "noir/recon.h"





static const char usage_str[] = "<kspace> <output> [<sensitivities>]";
static const char help_str[] =
		"Jointly estimate image and sensitivities with nonlinear\n"
		"inversion using {iter} iteration steps. Optionally outputs\n"
		"the sensitivities.";



int main_nlinv(int argc, char* argv[])
{
	bool normalize = true;
	float restrict_fov = -1.;
	const char* psf = NULL;
	struct noir_conf_s conf = noir_defaults;
	bool out_sens = false;
	bool scale_im = false;

	const struct opt_s opts[] = {

		OPT_UINT('i', &conf.iter, "iter", ""),
		OPT_SET('c', &conf.rvc, ""),<commit_msg>nlinv: add option for debug level<commit_after>/* Copyright 2013. The Regents of the University of California.
 * Copyright 2015-2016. <NAME>.
 * All rights reserved. Use of this source code is governed by
 * a BSD-style license which can be found in the LICENSE file.
 *
 * Authors: 
 * 2012-2016 <NAME> <<EMAIL>>
 */

#include <stdbool.h>
#include <complex.h>
#include <math.h>

#include "num/multind.h"
#include "num/flpmath.h"
#include "num/fft.h"
#include "num/init.h"

#include "misc/mri.h"
#include "misc/misc.h"
#include "misc/mmio.h"
#include "misc/utils.h"
#include "misc/opts.h"
#include "misc/debug.h"

#include "noir/recon.h"





static const char usage_str[] = "<kspace> <output> [<sensitivities>]";
static const char help_str[] =
		"Jointly estimate image and sensitivities with nonlinear\n"
		"inversion using {iter} iteration steps. Optionally outputs\n"
		"the sensitivities.";



int main_nlinv(int argc, char* argv[])
{
	bool normalize = true;
	float restrict_fov = -1.;
	const char* psf = NULL;
	struct noir_conf_s conf = noir_defaults;
	bool out_sens = false;
	bool scale_im = false;

	const struct opt_s opts[] = {

		OPT_UINT('i', &conf.iter, "iter", ""),
		OPT_INT('d', &debug_level, "level", "Debug level"),
		OPT_SET('c', &conf.rvc, ""),
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