Martin Uecker · Martin Uecker · H. Christian M. Holme · Martin Uecker · H. Christian M. Holme · Martin Uecker
--- a/.travis.yml
+++ b/.travis.yml
@@ -53,7 +53,7 @@ matrix:
        - sudo apt-get update -qq
        - sudo apt-get install -qq liblapacke-dev liblapack-dev

-    - env: OMP=0
+    - env: OMP=0 CFLAGS=-fblocks LDFLAGS=-lBlocksRuntime
      os: linux
      compiler: clang
      sudo: required
@@ -67,7 +67,7 @@ matrix:
        - make utest
      before_install:
        - sudo apt-get update -qq
-        - sudo apt-get install -qq liblapacke-dev
+        - sudo apt-get install -qq liblapacke-dev libblocksruntime-dev

    - env: OMP=1
      os: linux
@@ -99,7 +99,7 @@ matrix:
        - sudo apt-get update -qq
        - sudo apt-get install -qq liblapack-dev

-    - env: CUDA=1 CUDA_BASE=/usr/local/cuda-7.5/
+    - env: CUDA=1 CUDA_BASE=/usr/local/cuda-7.5/ CFLAGS=-fblocks LDFLAGS=-lBlocksRuntime
      os: linux
      compiler: clang-3.5
      sudo: required
@@ -114,7 +114,7 @@ matrix:
        - sudo apt-get update -qq
        - sudo apt-get install -qq clang-3.5
        - sudo apt-get install -qq --no-install-recommends cuda-drivers cuda-core-7.5 cuda-cudart-dev-7.5 cuda-cufft-dev-7.5 cuda-cublas-dev-7.5
-        - sudo apt-get install -qq liblapacke-dev
+        - sudo apt-get install -qq liblapacke-dev libblocksruntime-dev

    - env: BUILD_NAME="CMake"
      os: linux
@@ -156,7 +156,6 @@ matrix:

    - env: BUILD_NAME="CMake + CUDA" CUDA_BASE=/usr/local/cuda-7.5/
      os: linux
-      compiler: clang-3.5
      sudo: required
      dist: trusty
      addons:
@@ -196,16 +195,6 @@ matrix:
        - CC=gcc CXX=g++ cmake -DLINALG_VENDOR=LAPACKE -DLAPACKE_DIR=/usr/lib -DUSE_MATLAB=OFF -DUSE_CUDA=ON -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_BASE} ..
        - make

-    - env: MACPORTS=0
-      os: osx
-      compiler: gcc-4.8
-      script:
-        - make test
-        # make utest
-      before_install:
-        - brew update
-        - brew install fftw gcc48 homebrew/science/openblas
-
 script:
  - make bart
  - make all
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,7 +11,7 @@ enable_language(C)
 macro(use_c99)
  if (CMAKE_VERSION VERSION_LESS "3.1")
    if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
-      set (CMAKE_C_FLAGS "--std=gnu99 ${CMAKE_C_FLAGS}")
+      set (CMAKE_C_FLAGS "--std=gnu11 ${CMAKE_C_FLAGS}")
    endif ()
  else ()
    set (CMAKE_C_STANDARD 99)
@@ -264,20 +264,20 @@ install(TARGETS bartsupport
        ARCHIVE DESTINATION lib/static)


-## PASS #1:  Build stand-alone programs
-## Generate stand alone programs
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/StandAloneCode)
-foreach(curr_prog ${ALLPROGS})
-  CONFIG_BY_REPLACEMENT( ${CMAKE_CURRENT_LIST_DIR}/src/main.c ${CMAKE_CURRENT_BINARY_DIR}/StandAloneCode/${curr_prog}.c
-                         "/* Generated by cmake */"
-                         "main_real" "main_${curr_prog}")
-  bart_add_executable(${curr_prog} ${CMAKE_CURRENT_BINARY_DIR}/StandAloneCode/${curr_prog}.c ${CMAKE_CURRENT_LIST_DIR}/src/${curr_prog}.c)
-  target_link_libraries(${curr_prog} bartsupport )
-  install(TARGETS ${curr_prog}
-        RUNTIME DESTINATION bin
-        LIBRARY DESTINATION lib
-        ARCHIVE DESTINATION lib/static)
-endforeach()
+### PASS #1:  Build stand-alone programs
+### Generate stand alone programs
+#file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/StandAloneCode)
+#foreach(curr_prog ${ALLPROGS})
+#  CONFIG_BY_REPLACEMENT( ${CMAKE_CURRENT_LIST_DIR}/src/main.c ${CMAKE_CURRENT_BINARY_DIR}/StandAloneCode/${curr_prog}.c
+#                         "/* Generated by cmake */"
+#                        "main_real" "main_${curr_prog}")
+#  bart_add_executable(${curr_prog} ${CMAKE_CURRENT_BINARY_DIR}/StandAloneCode/${curr_prog}.c ${CMAKE_CURRENT_LIST_DIR}/src/${curr_prog}.c)
+#  target_link_libraries(${curr_prog} bartsupport )
+#  install(TARGETS ${curr_prog}
+#        RUNTIME DESTINATION bin
+#        LIBRARY DESTINATION lib
+#        ARCHIVE DESTINATION lib/static)
+#endforeach()

 ## More crafty file manipulation so that we maintain backward comaptibility
 ## with the Makefile
@@ -327,7 +327,7 @@ install(TARGETS bart

 #==============================================
 # TODO: Matlab code
-option(USE_MATLAB "Specify if the optional matlab programs should be built" ON)
+option(USE_MATLAB "Specify if the optional matlab programs should be built" OFF)
 if(USE_MATLAB)
  find_package(Matlab REQUIRED)
  if(MATLAB_FOUND)

--- a/LICENSE
+++ b/LICENSE
 Copyright (c) 2013-2017. The Regents of the University of California.
 Copyright (c) 2013-2017. BART Developer Team and Contributors.
-Copyright (c) 2012. Intel Coorperation. (src/lapacke/)
+Copyright (c) 2012. Intel Corporation. (src/lapacke/)
 All rights reserved.

 Redistribution and use in source and binary forms, with or without

--- a/Makefile
+++ b/Makefile
@@ -24,7 +24,7 @@ FFTWTHREADS?=1
 ISMRMRD?=0

 DESTDIR ?= /
-PREFIX ?= usr/
+PREFIX ?= usr/local/

 BUILDTYPE = Linux
 UNAME = $(shell uname -s)
@@ -91,7 +91,7 @@ CFLAGS ?= $(OPT) -Wmissing-prototypes
 CXXFLAGS ?= $(OPT)

 ifeq ($(BUILDTYPE), MacOSX)
-	CC ?= gcc-mp-4.7
+	CC ?= gcc-mp-6
 else
 	CC ?= gcc
 	# for symbols in backtraces

--- a/README
+++ b/README
@@ -49,6 +49,9 @@ Updates and further information can be found here:
 GCC compiler, the FFTW library, and optionally CUDA.
 (see recon/Makefile to turn options on or off)

+It should be possible to use the clang compiler, but older
+version before version 4.0 are known to cause problems.
+
 The software can be used in combination with Matlab or octave.


@@ -81,11 +84,11 @@ To install the required libraries on Debian and Ubuntu run:
 ### 2.1.2. Mac OS X

 Xcode is required and it is recommended to install a newer version 
-of gcc (4.7 seems to work) from MacPorts (http://www.macports.org/).
+of gcc from MacPorts (http://www.macports.org/).


    $ sudo port install fftw-3-single
-    $ sudo port install gcc47
+    $ sudo port install gcc6
    $ sudo port install libpng
    $ sudo port install openblas


--- a/debian/changelog
+++ b/debian/changelog
+bart (0.4.03-1) UNRELEASED; urgency=medium
+
+  * New upstream version.
+  * Update copyright file.
+  * Fix install.
+  * Standards-Version: 4.1.4
+  * Secure url for copyright format.
+
+ -- Martin Uecker <martin.uecker@med.uni-goettingen.de>  Fri, 27 Apr 2018 21:34:11 +0200
+
 bart (0.4.02-2) unstable; urgency=medium

  * Turn off unit tests on some architectures.

--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 10),
               liblapack-dev | liblapack.so,
               libpng-dev,
               liblapacke-dev
-Standards-Version: 4.1.1
+Standards-Version: 4.1.4
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bart.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/bart.git
 Homepage: https://mrirecon.github.io/bart/

--- a/debian/copyright
+++ b/debian/copyright
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: BART
 Upstream-Contact: Martin Uecker <martin.uecker@med.uni-goettingen.de>
 Source: https://github.com/mrirecon/bart

 Files: *
-Copyright: 2013-2017 The Regents of the University of California
-           2015-2017 Martin Uecker
+Copyright: 2013-2018 The Regents of the University of California
+           2015-2018 Martin Uecker
           2017      Massachusetts Institute of Technology
           2017      University of Oxford
           2012,2017 Intel Corporation
@@ -15,7 +15,7 @@ Copyright: 2013-2017 The Regents of the University of California
 	   2016	     David Smith
           2016      Hans Johnson
           2017      Nguyen Damien
-           2017      Christian Holme
+           2017-2018 Christian Holme
           2017      Sebastian Rosenzweig
 License: BSD-3-clause
 All rights reserved.

--- a/debian/patches/0001-remove-empty-directory.patch
+++ b/debian/patches/0001-remove-empty-directory.patch
@@ -7,7 +7,7 @@ Subject: remove empty directory
 1 file changed, 1 deletion(-)

 diff --git a/Makefile b/Makefile
-index 834698d..72b1829 100644
+index bccc92c..eeceb3d 100644
 --- a/Makefile
 +++ b/Makefile
 @@ -495,7 +495,6 @@ install: bart $(root)/doc/commands.txt

--- a/debian/patches/0002-bump-version.patch
+++ b/debian/patches/0002-bump-version.patch
-From: Martin Uecker <martin.uecker@med.uni-goettingen.de>
-Date: Sun, 26 Nov 2017 12:57:46 +0100
-Subject: bump version
-
---
- version.txt | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/version.txt b/version.txt
-index 26a1a7e..495f58b 100644
--- a/version.txt
-+++ b/version.txt
-@@ -1 +1 @@
-v0.4.01
-+v0.4.02
--- a/debian/patches/series
+++ b/debian/patches/series
 0001-remove-empty-directory.patch
-0002-bump-version.patch
--- a/debian/rules
+++ b/debian/rules
@@ -12,6 +12,9 @@ NOTEST_ARCHS=i386 mips mipsel hurd-i386 kfreebsd-i386 m68k sh4
 %:
 	dh $@

+override_dh_install:
+	PREFIX=$(shell pwd)/debian/$(NAME) make install
+
 override_dh_auto_test:
 ifeq (,$(filter $(NOTEST_ARCHS), $(DEB_BUILD_ARCH)))
 	make utest

--- a/doc/references.txt
+++ b/doc/references.txt
@@ -12,11 +12,15 @@ Software Toolbox and Programming Library for Compressed Sensing and
 Parallel Imaging,
 ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2013.

+Tamir JI, Ong F, Cheng JY, Uecker M, Lustig M. Generalized Magnetic
+Resonance Image Reconstruction using The Berkeley Advanced
+Reconstruction Toolbox,
+ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2016.



 - sensitivity-encoded parallel imaging -
-(commands: itsense, pocsense, bpsense, rsense, pics)
+(commands: itsense, pocsense, bpsense, pics)


 Ra JB and Rim CY.
@@ -58,6 +62,11 @@ trajectories.
 Annual Meeting of the ISMRM, Glasgow 2001,
 In: Proc Intl Soc Mag Reson Med 9; 767.

+Uecker M, Zhang S, Frahm J.
+Nonlinear Inverse Reconstruction for Real-time MRI of the
+Human Heart Using Undersampled Radial FLASH.
+Magn Reson Med 2010; 63:1456-1462.
+
 Ong F, Uecker M, Jiang W, Lustig M.
 Fast Non-Cartesian Reconstruction with Pruned Fast Fourier Transform.
 Annual Meeting ISMRM, Toronto 2015,
@@ -119,6 +128,11 @@ Calibrationless Parallel Imaging Reconstruction Based on Structured
 Low-Rank Matrix Completion.
 Magn Reson Med 2014; 72:959-970.

+Holme HCM, Rosenzweig S, Ong F, Wilke RN, Lustig M, Uecker M.
+ENLIVE: An Efficient Nonlinear Method for Calibrationless and
+Robust Parallel Imaging.
+arXiv:1706.09780 [physics.med-ph]
+



@@ -169,7 +183,7 @@ Magn Reson Med 2009; 61:145-152.


 - sparsity transforms, variational penalties, regularization -
-(commands: cdf97, rof, lrmatrix, pocsense, rsense, pics)
+(commands: cdf97, rof, lrmatrix, pocsense, pics)


 Rudin LI, Osher S, Fatemi E.
@@ -177,7 +191,7 @@ Nonlinear total variation based noise removal algorithms,
 Physica D: Nonlinear Phenomena 1992; 60:259-268.

 Figueiredo MAT and Nowak RD.
-An EM algorithm for wavelet-based image restoration
+An EM algorithm for wavelet-based image restoration.
 IEEE Trans Image Process 2003; 12:906-916.

 Ong F, Uecker M, Tariq U, Hsiao A, Alley MT, Vasanawala SS, Lustig M.
@@ -186,8 +200,7 @@ Magn Reson Med 2015; 73:828-842.

 Ong F, Lustig M.
 Beyond low rank + sparse: Multi-scale low rank matrix decomposition,
-preprint 2015; arXiv:1507.08751.
-
+IEEE J Sel Topics Signal Process 2016; 10:672-687.



@@ -283,10 +296,25 @@ Radiology 2016; 278:245-256.
 Cheng JY, Hanneman K, Zhang T, Alley MT, Lai P, Tamir JI, Uecker M,
 Pauly JM, Lustig M, Vasanawala SS.
 Comprehensive Motion-Compensated Highly-Accelerated 4D Flow MRI with
-Ferumoxytol Enhancement for Pediatric Congenital Heart Disease,
-J Magn Reson Imaging, Epub (2015)
+Ferumoxytol Enhancement for Pediatric Congenital Heart Disease.
+J Magn Reson Imaging 2016; 43:1355-1368.

 Tamir JI, Uecker M, Chen W, Lai P, Aleey MT, Vasanawala SS, Lustig M.
-T2-Shuffling: Sharp, Multi-Contrast, Volumetric Fast Spin-Echo Imaging
-Magn Recon Med; in press (2015).
+T2-Shuffling: Sharp, Multi-Contrast, Volumetric Fast Spin-Echo Imaging.
+Magn Recon Med 2017; 77:180-195.
+
+Uecker M, Lustig M.
+Estimating Absolute-Phase Maps Using ESPIRiT and Virtual Conjugate Coils.
+Magn Reson Med 2017; 77:1201-1207.
+
+Moghari MH, Uecker M, Roujol S, Sabbagh M, Geva T, Powell AJ.
+Accelerated Whole-heart Magnetic Resonance Angiography Using
+a Variable-Density Poisson-Disc Undersampling Pattern and
+Compressed Sensing Reconstruction.
+Magn Reson Med 2018; 79:761-769.
+
+Cheng JY, Zhang T, Alley MT, Uecker M, Lustig M, Pauly JM, Vasanawala SS.
+Comprehensive Multi-Dimensional MRI for the Simultaneous Assessment
+of Cardiopulmonary Anatomy and Physiology.
+Scientific Reports 2017; 7:5330.

--- a/rules/misc.mk
+++ b/rules/misc.mk
@@ -19,4 +19,4 @@ DOTHIS := $(shell $(root)/rules/update-version.sh)
 $(srcdir)/misc/version.o: $(srcdir)/misc/version.inc


-UTARGETS += test_pattern
+UTARGETS += test_pattern test_types
--- a/rules/num.mk
+++ b/rules/num.mk
@@ -18,5 +18,5 @@ lib/libnum.a: libnum.a($(numobjs))


 UTARGETS += test_multind test_flpmath test_splines test_linalg test_polynom test_window
-UTARGETS += test_blas
+UTARGETS += test_blas test_mdfft

--- a/scripts/espirit_econ.sh
+++ b/scripts/espirit_econ.sh
+#!/bin/bash
+# Copyright 2018. Martin Uecker.
+# All rights reserved. Use of this source code is governed by
+# a BSD-style license which can be found in the LICENSE file.
+#
+# Authors:
+# 2018 Martin Uecker <martin.uecker@med.uni-goettingen.de>
+#
+# Memory-saving ESPIRiT
+#
+set -e
+
+LOGFILE=/dev/stdout
+
+title=$(cat <<- EOF
+	ESPIRiT-ECON
+EOF
+)
+
+helpstr=$(cat <<- EOF
+-l logfile
+-h help
+EOF
+)
+
+usage="Usage: $0 [-h] <kspace> <output>"
+
+echo "$title"
+echo
+
+while getopts "hl:" opt; do
+        case $opt in
+	h)
+		echo "$usage"
+		echo
+		echo "$helpstr"
+		exit 0
+	;;
+	l)
+		LOGFILE=$(readlink -f "$OPTARG")
+	;;
+        \?)
+        	echo "$usage" >&2
+		exit 1
+        ;;
+        esac
+done
+
+shift $((OPTIND - 1))
+
+
+if [ $# -lt 2 ] ; then
+
+        echo "$usage" >&2
+        exit 1
+fi
+
+
+export PATH=$TOOLBOX_PATH:$PATH
+
+input=$(readlink -f "$1")
+output=$(readlink -f "$2")
+
+if [ ! -e $input.cfl ] ; then
+	echo "Input file does not exist." >&2
+	echo "$usage" >&2
+	exit 1
+fi
+
+if [ ! -e $TOOLBOX_PATH/bart ] ; then
+        echo "\$TOOLBOX_PATH is not set correctly!" >&2
+	exit 1
+fi
+
+
+#WORKDIR=$(mktemp -d)
+# Mac: http://unix.stackexchange.com/questions/30091/fix-or-alternative-for-mktemp-in-os-x
+WORKDIR=`mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir'`
+trap 'rm -rf "$WORKDIR"' EXIT
+cd $WORKDIR
+
+# start group for redirection of output to the logfile
+{
+
+XX=$(bart show -d0 $input)
+YY=$(bart show -d1 $input)
+ZZ=$(bart show -d2 $input)
+
+DIM=2
+# To decouple along another dimension:
+# 1. change DIM
+# 2. replace ZZ below
+# 3. change the ecaltwo command
+
+bart ecalib -1 $input eon
+
+# zero-pad
+bart fft $(bart bitmask ${DIM}) eon eon_fft
+bart resize -c ${DIM} ${ZZ} eon_fft eon_fft2
+bart fft -i $(bart bitmask ${DIM}) eon_fft2 eon
+
+for i in `seq -w 0 $(($ZZ - 1))` ; do
+	
+	bart slice ${DIM} $i eon sl
+	bart ecaltwo ${XX} ${YY} 1 sl sens-$i.coo
+done
+
+# # join slices back together
+bart join ${DIM} sens-*.coo $output
+
+} > $LOGFILE
+
+exit 0
--- a/src/bart.c
+++ b/src/bart.c
@@ -60,11 +60,12 @@ int main_bart(int argc, char* argv[])
 			exit(1);
 		}

-		const char* tpath[3] = {
-
+		const char* tpath[] = {
+#ifdef TOOLBOX_PATH_OVERRIDE
 			getenv("TOOLBOX_PATH"),
-			"/usr/lib/bart/commands/",
+#endif
 			"/usr/local/lib/bart/commands/",
+			"/usr/lib/bart/commands/",
 		};

 		for (unsigned int i = 0; i < ARRAY_SIZE(tpath); i++) {

--- a/src/bench.c
+++ b/src/bench.c
 /* Copyright 2014. The Regents of the University of California.
- * Copyright 2015-2017. Martin Uecker.
+ * Copyright 2015-2018. Martin Uecker.
 * All rights reserved. Use of this source code is governed by
 * a BSD-style license which can be found in the LICENSE file.
 * 
 * Authors: 
- * 2014-2017 Martin Uecker <martin.uecker@med.uni-goettingen.de>
+ * 2014-2018 Martin Uecker <martin.uecker@med.uni-goettingen.de>
 * 2014 Jonathan Tamir <jtamir@eecs.berkeley.edu>
 */

@@ -19,6 +19,8 @@
 #include "num/rand.h"
 #include "num/init.h"
 #include "num/ops.h"
+#include "num/mdfft.h"
+#include "num/fft.h"

 #include "wavelet/wavthresh.h"

@@ -414,6 +416,94 @@ static double bench_wavelet(long scale)
 }


+static double bench_generic_mdfft(long dims[DIMS], unsigned long flags)
+{
+	complex float* x = md_alloc(DIMS, dims, CFL_SIZE);
+	complex float* y = md_alloc(DIMS, dims, CFL_SIZE);
+
+	md_gaussian_rand(DIMS, dims, x);
+
+	double tic = timestamp();
+
+	md_fft(DIMS, dims, flags, 0u, y, x);
+
+	double toc = timestamp();
+
+	md_free(x);
+	md_free(y);
+
+	return toc - tic;
+}
+
+static double bench_mdfft(long scale)
+{
+	long dims[DIMS] = { 1, 128 * scale, 128 * scale, 1, 1, 4, 1, 4 };
+	return bench_generic_mdfft(dims, 6ul);
+}
+
+
+
+static double bench_generic_fft(long dims[DIMS], unsigned long flags)
+{
+	complex float* x = md_alloc(DIMS, dims, CFL_SIZE);
+	complex float* y = md_alloc(DIMS, dims, CFL_SIZE);
+
+	md_gaussian_rand(DIMS, dims, x);
+
+	double tic = timestamp();
+
+	fft(DIMS, dims, flags, y, x);
+
+	double toc = timestamp();
+
+	md_free(x);
+	md_free(y);
+
+	return toc - tic;
+}
+
+
+
+static double bench_fft(long scale)
+{
+	long dims[DIMS] = { 1, 256 * scale, 256 * scale, 1, 1, 16, 1, 8 };
+	return bench_generic_fft(dims, 6ul);
+}
+
+
+
+
+static double bench_generic_fftmod(long dims[DIMS], unsigned long flags)
+{
+	complex float* x = md_alloc(DIMS, dims, CFL_SIZE);
+	complex float* y = md_alloc(DIMS, dims, CFL_SIZE);
+
+	md_gaussian_rand(DIMS, dims, x);
+
+	double tic = timestamp();
+
+	fftmod(DIMS, dims, flags, y, x);
+
+	double toc = timestamp();
+
+	md_free(x);
+	md_free(y);
+
+	return toc - tic;
+}
+
+
+
+static double bench_fftmod(long scale)
+{
+	long dims[DIMS] = { 1, 256 * scale, 256 * scale, 1, 1, 16, 1, 16 };
+	return bench_generic_fftmod(dims, 6ul);
+}
+
+
+
+
+
 enum bench_indices { REPETITION_IND, SCALE_IND, THREADS_IND, TESTS_IND, BENCH_DIMS };

 typedef double (*bench_fun)(long scale);
@@ -472,6 +562,9 @@ const struct benchmark_s {
 	{ bench_copy1,		"copy 1" },
 	{ bench_copy2,		"copy 2" },
 	{ bench_wavelet,	"wavelet soft thresh" },
+	{ bench_mdfft,		"(MD-)FFT" },
+	{ bench_fft,		"FFT" },
+	{ bench_fftmod,		"fftmod" },
 };



--- a/src/cabs.c
+++ b/src/cabs.c
@@ -11,6 +11,7 @@
 #include <complex.h>
 #include <stdio.h>

+#include "num/init.h"
 #include "num/flpmath.h"

 #include "misc/mmio.h"
@@ -28,6 +29,8 @@ int main_cabs(int argc, char* argv[])
 {
 	mini_cmdline(&argc, argv, 2, usage_str, help_str);

+	num_init();
+
 	long dims[DIMS];

 	complex float* idata = load_cfl(argv[1], DIMS, dims);

--- a/src/calib/calib.c
+++ b/src/calib/calib.c
@@ -514,6 +514,7 @@ void calib2(const struct ecalib_conf* conf, const long out_dims[DIMS], complex f

 	if (conf->rotphase) {

+		// rotate the the phase with respect to the first principle component
 		long scc_dims[DIMS] = MD_INIT_ARRAY(DIMS, 1);
 		scc_dims[COIL_DIM] = channels;
 		scc_dims[MAPS_DIM] = channels;
@@ -564,7 +565,6 @@ void calib2(const struct ecalib_conf* conf, const long out_dims[DIMS], complex f
 	debug_printf(DP_DEBUG1, "Fix phase...\n");


-	// rotate the the phase with respect to the first principle component
 	fixphase2(DIMS, out_dims, COIL_DIM, rot[0], out_data, out_data);

 	md_free(imgcov);