sync code with internal version

	- size reduction: compile multiple tools into one 'bart' binary
	- size reduction: do not compile with debugging by default
	- use -framework Accelerate instead of -f.. vecLib to fix
	  compilation for MacOS X Yosemite
	- Makefile: add compile-time OMP option for OpenMP

	- 'bart.m' matlab script to simplify calling of tools
	- mat2cfl: new tool to import certain matlab data files
	- nlinv: add option for real-value constrained reconstruction
	- normalize: normalize using l1 norm
	- ecalib/ecaltwo: option normalize sensitivities using l1 norm
	- (still commented out: normalize phase according to max. variance)

	- add power iteration algorithm
	- 'normalizel1' function to normalize using l1 norm
	- functions to construct matrix from non-overlapping blocks
	- add functions 'md_zarg' / 'md_zexpj'
	- fix 'md_zsadd' to take a complex scalar
	- runtime option to turn off cuda memory caching
	- MD_BIT, ..., bit fiddling macros
	- eliminate hard dependency on GSL in gridding code
	- other minor changes and enhancements

Makefile

@@ -13,14 +13,18 @@ CUDA=0
 ACML=0
 CULA=0
 GSL=1
+OMP=1
 
 BUILDTYPE = Linux
 UNAME = $(shell uname -s)
 NNAME = $(shell uname -n)
 
+MYLINK=ln
+
 ifeq ($(UNAME),Darwin)
 	BUILDTYPE = MacOSX
 	ACML = 0
+	MYLINK = ln -s
 endif
 
 ARFLAGS = r
@@ -49,13 +53,12 @@ ALLDEPS = $(shell find $(srcdir) -name ".*.d")
 
 OPT = -O3 -ffast-math 
 CPPFLAGS = $(DEPFLAG) -Wall -Wextra -I$(srcdir)/ 
-CFLAGS = -g $(OPT) -std=c99 -Wmissing-prototypes -fopenmp -I$(srcdir)/
-CXXFLAGS = -g $(OPT) -fopenmp -I$(srcdir)/
+CFLAGS = $(OPT) -std=c99 -Wmissing-prototypes -I$(srcdir)/
+CXXFLAGS = $(OPT) -I$(srcdir)/
 CC = gcc
 CXX = g++
 
 
-
 #ifeq ($(BUILDTYPE), MacOSX)
 #	CC = gcc-mp-4.7
 #endif
@@ -85,13 +88,18 @@ acml.top := /usr/local/acml/acml4.4.0/gfortran64_mp/
 
 fftw.top := /usr/
 
+# Matlab
+
+matlab.top := /usr/local/matlab/
+
 # ISMRM
 
 ismrm.top := /usr/local/ismrmrd/
 
 
 
 
+
 # Main build targets
 
 TBASE=slice crop resize join transpose zeros ones flip circshift extract repmat bitmask
@@ -101,8 +109,9 @@ TRECO=sense pocsense rsense bpsense itsense nlinv nufft rof nusense
 TCALIB=ecalib caldir walsh cc
 TMRI=rss homodyne pattern poisson twixread
 TSIM=phantom traj
-TARGETS = $(TBASE) $(TFLP) $(TNUM) $(TRECO) $(TCALIB) $(TMRI) $(TSIM) $(TIO)
-
+BTARGETS = $(TBASE) $(TFLP) $(TNUM)
+XTARGETS = bart $(TRECO) $(TCALIB) $(TMRI) $(TSIM)
+TARGETS = $(BTARGETS) $(XTARGETS)
 
 
 
@@ -125,14 +134,12 @@ MODULES_nufft = -lnoncart -liter -llinops
 MODULES_rof = -liter -llinops
 MODULES_bench = -lwavelet2 -lwavelet3 -llinops
 MODULES_phantom = -lsimu
+MODULES_bart += -lbox -lwavelet2 -lwavelet3 -llinops
 
 
 -include Makefile.$(NNAME)
 -include Makefile.local
 
-ifeq ($(ACML),1)
-TARGETS += $(TLOWRANK)
-endif
 
 
 
@@ -162,7 +169,7 @@ ifeq ($(CUDA),1)
 CUDA_H := -I$(cuda.top)/include
 CPPFLAGS += -DUSE_CUDA $(CUDA_H)
 ifeq ($(BUILDTYPE), MacOSX)
-CUDA_L := -L$(cuda.top)/lib -lcufft -lcudart -lcublas -lcuda -m64
+CUDA_L := -L$(cuda.top)/lib -lcufft -lcudart -lcublas -lcuda -m64 -lstdc++
 else
 CUDA_L := -L$(cuda.top)/lib64 -lcufft -lcudart -lcublas -lcuda -lstdc++
 endif 
@@ -171,7 +178,7 @@ CUDA_H :=
 CUDA_L :=  
 endif
 
-NVCCFLAGS = -DUSE_CUDA -Xcompiler -fPIC -Xcompiler -fopenmp -O3 -arch=sm_20 -I$(srcdir)/ -m64
+NVCCFLAGS = -DUSE_CUDA -Xcompiler -fPIC -Xcompiler -fopenmp -O3 -arch=sm_20 -I$(srcdir)/ -m64 -ccbin $(CC)
 #NVCCFLAGS = -Xcompiler -fPIC -Xcompiler -fopenmp -O3  -I$(srcdir)/
 
 
@@ -181,6 +188,16 @@ NVCCFLAGS = -DUSE_CUDA -Xcompiler -fPIC -Xcompiler -fopenmp -O3 -arch=sm_20 -I$(
 
 
 
+ifeq ($(OMP),1)
+CFLAGS += -fopenmp
+CXXFLAGS += -fopenmp
+else
+CFLAGS += -Wno-unknown-pragmas
+CXXFLAGS += -Wno-unknown-pragmas
+endif
+
+
+
 # cula
 
 ifeq ($(CULA),1)
@@ -217,11 +234,11 @@ BLAS_L :=
 
 ifeq ($(ACML),1)
 BLAS_H := -I$(acml.top)/include
-BLAS_L := $(wildcard $(acml.top)/lib/*.a) -lgfortran
+BLAS_L := -L$(acml.top)/lib -lgfortran -lacml_mp -Wl,-rpath $(acml.top)/lib
 CPPFLAGS += -DUSE_ACML
 else
 ifeq ($(BUILDTYPE), MacOSX)
-BLAS_L := -lblas -framework vecLib 
+BLAS_L := -lblas -framework Accelerate
 else
 BLAS_L := -llapack -lblas
 endif
@@ -238,8 +255,7 @@ FFTW_L := -L$(fftw.top)/lib -lfftw3f_threads -lfftw3f
 # Matlab
 
 MATLAB_H := -I$(matlab.top)/extern/include
-MATLAB_L := -Wl,-rpath-link,$(matlab.top)/bin/glnxa64 -L$(matlab.top)/bin/glnxa64 -lmat -lmx -lm -lstdc++
-
+MATLAB_L := -Wl,-rpath $(matlab.top)/bin/glnxa64 -L$(matlab.top)/bin/glnxa64 -lmat -lmx -lm -lstdc++
 
 # ISMRM
 
@@ -267,16 +283,26 @@ all: $(TARGETS)
 
 
 
-# special ismrmrd target
+# special targets
+
+
+bart: CPPFLAGS += -DMAIN_LIST="$(BTARGETS:%=%,) ()"
+
 
 ismrmrd: $(srcdir)/ismrmrd.c -lismrm -lnum -lmisc
 	$(CC) $(CXXFLAGS) -o ismrmrd $+ $(CUDA_L) $(ISMRM_L) -lstdc++ -lm
 
+mat2cfl: $(srcdir)/mat2cfl.c -lnum -lmisc
+	$(CC) $(CFLAGS) $(MATLAB_H) -omat2cfl  $+ $(MATLAB_L) $(CUDA_L)
+
+
+$(BTARGETS): bart
+	rm -f $@ && $(MYLINK) bart $@
 
 
 .SECONDEXPANSION:
-$(TARGETS): % : $(srcdir)/%.c $$(MODULES_%) $(MODULES)
-	$(CC) $(CPPFLAGS) $(CFLAGS) -Dmain_$@=main -o $@ $+ $(FFTW_L) $(CUDA_L) $(CULA_L) $(BLAS_L) $(GSL_L) -lm -lstdc++ -lpng
+$(XTARGETS): % : $(srcdir)/%.c $$(MODULES_%) $(MODULES)
+	$(CC) $(CPPFLAGS) $(CFLAGS) -Dmain_$@=main -o $@ $+ $(FFTW_L) $(CUDA_L) $(CULA_L) $(BLAS_L) $(GSL_L) -lm #-lpng
 #	rm $(srcdir)/[email protected]
 
 

README

@@ -84,20 +84,24 @@ install the ISMRM Raw Data format library (http://ismrmrd.sourceforge.net/).
 
 Organization:
 
-recon/			main directory / built software tools
-recon/Makefile		Makefile
-recon/matlab 		Matlab helper scripts 
-recon/src/		source code
-recon/src/calib 	source code for sensitivity calibration
-recon/src/sense		source code for SENSE or ESPIRiT reconstruction
-recon/src/noir		source code for nonlinear inversion
-recon/src/sake		source code for SAKE reconstruction
-recon/src/wavelet2	source code for wavelets
-recon/src/num		base library with numerical functions
-recon/src/iter		iterative algorithms
-recon/src/misc		miscellaneous (e.g. I/O)
-recon/src/ismrm		support for ISMRM raw data format
-recon/lib/		built software libraries
+.		main directory / built software tools
+Makefile	Makefile
+matlab/		Matlab helper scripts
+python/		Python helper functions
+doc/		documentation
+src/		source code
+src/calib 	source code for sensitivity calibration
+src/sense	source code for SENSE or ESPIRiT reconstruction
+src/noir	source code for nonlinear inversion
+src/sake	source code for SAKE reconstruction
+src/wavelet2	source code for wavelets
+src/wavelet3	source code for new wavelets (experimental)
+src/num		base library with numerical functions
+src/iter	iterative algorithms
+src/linops	library of linear operators
+src/misc	miscellaneous (e.g. I/O)
+src/ismrm	support for ISMRM raw data format
+lib/		built software libraries
 
 
 
@@ -175,7 +179,7 @@ dimensions run from 0 to N-1. Sometimes a set of dimensions is given
 as a bitmask where the lowest bit corresponds to the 0st dimension.
 
 
-For example, a Fourier transform of first three dimemensions can
+For example, an inverse Fourier transform of first three dimensions can
 be performed with the following command:
 
 

doc/commands.txt

@@ -200,7 +200,8 @@ ecalib [-t threshold] [-c crop_value] [-k kernel_size] [-r cal_size] [-m maps] <
 	-k ksize	kernel size
 	-r cal_size	Limits the size of the calibration region.
 	-m maps		Number of maps to compute.
-	-1 perform only first part of the calibration
+	-I		intensity correction
+	-1		perform only first part of the calibration
 
 
 ecaltwo [-c crop] [-m maps] x y z <input> <sensitivities> [<ev_maps>]

matlab/bart.m

@@ -0,0 +1,43 @@
+% 2014 Martin Uecker <[email protected]>
+
+function [varargout] = bart(cmd, varargin);
+
+	if isempty(getenv('TOOLBOX_PATH'))
+		error('Environment variable TOOLBOX_PATH is not set.');
+	end
+
+	if ismac==1
+		setenv('DYLD_LIBRARY_PATH', '');
+	else
+		setenv('LD_LIBRARY_PATH', '');
+	end
+
+	name = tempname;
+
+	in = cell(1, nargin - 1);
+
+	for i=1:nargin - 1,
+		in{i} = strcat(name, 'in', num2str(i));
+		writecfl(in{i}, varargin{i});
+	end
+
+	out = cell(1, nargout);
+
+	for i=1:nargout,
+		out{i} = strcat(name, 'out', num2str(i));
+	end
+
+	system([getenv('TOOLBOX_PATH'), '/', cmd, ' ', strjoin(in, ' '), ' ', strjoin(out, ' ')]);
+
+	for i=1:nargin - 1,
+		delete(strcat(in{i}, '.cfl'));
+		delete(strcat(in{i}, '.hdr'));
+	end
+
+	for i=1:nargout,
+		varargout{i} = readcfl(out{i});
+		delete(strcat(out{i}, '.cfl'));
+		delete(strcat(out{i}, '.hdr'));
+	end
+end
+

rules/box.mk

@@ -0,0 +1,13 @@
+
+
+
+boxsrcs := $(BTARGETS:%=src/%.c)
+boxobjs := $(boxsrcs:.c=.o)
+
+.INTERMEDIATE: $(boxobjs)
+
+lib/libbox.a: libbox.a($(boxobjs))
+lib/libbox.a: CFLAGS += -Wno-missing-prototypes
+
+
+

src/bart.c

@@ -0,0 +1,77 @@
+/* Copyright 2015. The Regents of the University of California.
+ * 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 Martin Uecker <[email protected]>
+ */
+
+#include <stdlib.h>
+#include <assert.h>
+#include <stdio.h>
+#include <string.h>
+#include <libgen.h>
+
+#include "misc/misc.h"
+#include "misc/cppmap.h"
+
+
+#define DECLMAIN(x) \
+extern int main_ ## x(int argc, char* argv[]);
+MAP(DECLMAIN, MAIN_LIST)
+#undef	DECLMAIN
+
+struct {
+
+	int (*main_fun)(int argc, char* argv[]);
+	const char* name;
+
+} dispatch_table[] = {
+
+#define DENTRY(x) { main_ ## x, # x },
+	MAP(DENTRY, MAIN_LIST)
+#undef  DENTRY
+	{ NULL, NULL }
+};
+
+static void usage(void)
+{
+	printf("BART. Available commands are:");
+
+	for (int i = 0; NULL != dispatch_table[i].name; i++) {
+
+		if (0 == i % 6)
+			printf("\n");
+
+		printf("%-12s", dispatch_table[i].name);
+	}
+
+	printf("\n");
+}
+
+int main(int argc, char* argv[])
+{
+	char* bn = basename(argv[0]);
+
+	if (0 == strcmp(bn, "bart")) {
+
+		if (1 == argc) {
+
+			usage();
+			exit(1);
+		}
+
+		return main(argc - 1, argv + 1);
+	}
+
+	for (int i = 0; NULL != dispatch_table[i].name; i++) {
+
+		if (0 == strcmp(bn, dispatch_table[i].name))
+			return dispatch_table[i].main_fun(argc, argv);
+	}
+
+	fprintf(stderr, "Unknown command.\n");
+	exit(1);
+}
+
+