sync code with internal version

	- extended coil compression tool cc as replacement for scc
	   - geometric coil compression and
	   - preliminary version of ESPIRiT-based compression
	- spow (point-wise power) and cpyphs (copy phase) tools
	- resize tool can process multiple dimensions at once
	- fix missing lib directory for github version
	- other minor fixes and extensions

Makefile

@@ -95,11 +95,11 @@ ismrm.top := /usr/local/ismrmrd/
 # Main build targets
 
 TBASE=slice crop resize join transpose zeros ones flip circshift extract repmat bitmask
-TFLP=scale conj fmac saxpy sdot conv
-TNUM=fft fftmod noise bench threshold creal
+TFLP=scale conj fmac saxpy sdot spow cpyphs creal
+TNUM=fft fftmod noise bench threshold conv
 TRECO=sense pocsense rsense bpsense itsense nlinv nufft rof nusense
-TCALIB=ecalib caldir walsh
-TMRI=rss homodyne pattern scc poisson twixread
+TCALIB=ecalib caldir walsh cc
+TMRI=rss homodyne pattern poisson twixread
 TSIM=phantom traj
 TARGETS = $(TBASE) $(TFLP) $(TNUM) $(TRECO) $(TCALIB) $(TMRI) $(TSIM) $(TIO)
 
@@ -120,6 +120,7 @@ MODULES_itsense = -liter -llinops
 MODULES_ecalib = -lcalib
 MODULES_caldir = -lcalib
 MODULES_walsh = -lcalib
+MODULES_cc = -lcalib
 MODULES_nufft = -lnoncart -liter -llinops
 MODULES_rof = -liter -llinops
 MODULES_bench = -lwavelet2 -llinops

README

@@ -278,6 +278,11 @@ saxpy scale <input1> <input2> <output>
 	Multiply input1 with scale factor and add input2.
 
 
+spow exponent <input> <output>
+
+	Raise array to the power of {exponent}. The exponent can be a complex number.
+
+
 fmac [-A] [-C] [-s bitmask] <input1> <input2> <output>
 
 	Multiply and accumulate.
@@ -292,6 +297,11 @@ conj <input> <output>
 	Compute complex conjugate.
 
 
+cpyphs <input> <output
+
+	Copy phase from <input> to <output>.
+
+
 fft [-u] [-i] bitmask <input> <output>
 
 	Performs a fast Fourier transform (FFT) along dimensions
@@ -380,14 +390,14 @@ ecaltwo [-c crop] [-m maps] x y z <input> <sensitivities> [<ev_maps>]
 	-m maps		Number of maps to compute.
 
 
-scc [-v] [-A] [-r cal_size] [-P num_coeffs] <kspace> <coeff>|<proj_kspace>
+cc [-A] [-r cal_size] [-P num_coeffs] <kspace> <coeff>|<proj_kspace>
 
 	Performs simple coil compression.
 
 	-P N	perform compression to N virtual channels
 	-r S	size of calibration region
 	-A	use all data to compute coefficients
-	-v	verbose
+	-S|G|E	type: SVD, Geometric, ESPIRiT
 	-h	help
 
 
@@ -419,7 +429,7 @@ nusense [-l1/-l2] [-r lambda] <traj> <kspace> <sensitivities> <output>
 	-r lambda	regularization parameter
 
 
-bpsense [-g] [-r l2lambda] [-c] [-e eps] [-u rho] <kspace> <sensitivities> <output>
+bpsense [-r l2lambda] [-c] [-e eps] [-u rho] <kspace> <sensitivities> <output>
 
 	Perform basis pursuit denoising for SENSE/ESPIRiT reconstruction:
 	min_x ||T x||_1 + lambda/2 ||x||_2^2 subject to: ||y - Ax||_2 <= eps
@@ -429,7 +439,7 @@ bpsense [-g] [-r l2lambda] [-c] [-e eps] [-u rho] <kspace> <sensitivities> <outp
 	-u rho	ADMM penalty parameter
 	-c	real-value constraint
 	-t	use TV norm
-	-F	truth image
+	-T	truth image
 
 
 nlinv [-i iterations] <kspace> <output> [<sens>]
@@ -479,7 +489,7 @@ rof lambda bitmask <input> <output>
 
 poisson <outfile>
 
-Computes Poisson-disc sampling pattern.
+	Computes Poisson-disc sampling pattern.
 
 	-X	size dimension 0 (readout)
 	-Y	size dimension 1 (phase)
@@ -526,6 +536,8 @@ twixread [...] [-a A] <dat file> <output>
 	-s S	number of slices
 	-c C	number of channels
 	-a A	total number of ADCs
+	-L	use linectr offset
+	-P	use partctr offset
 	-h	help
 
 

src/bpsense.c

@@ -43,7 +43,7 @@
 
 static void usage(const char* name, FILE* fd)
 {
-	fprintf(fd, "Usage: %s [-g] [-r l2lambda] [-c] [-e eps] [-u rho] <kspace> <sensitivities> <output>\n", name);
+	fprintf(fd, "Usage: %s [-r l2lambda] [-c] [-e eps] [-u rho] <kspace> <sensitivities> <output>\n", name);
 }
 
 static void help(void)
@@ -57,7 +57,7 @@ static void help(void)
 		"-u rho\tADMM penalty parameter\n"
 		"-c\treal-value constraint\n"
 		"-t\tuse TV norm\n"
-		"-F\ttruth image\n");
+		"-T\ttruth image\n");
 }
 
 
@@ -75,18 +75,20 @@ int main(int argc, char* argv[])
 
 	bool usegpu = false;
 	const char* psf = NULL;
-	char image_truth_fname[100];
-	_Bool im_truth = false;
-	_Bool use_tvnorm = false;
+	const char* image_truth_fname = NULL;
+	bool im_truth = false;
+	bool use_tvnorm = false;
 
 	double start_time = timestamp();
 
 	int c;
-	while (-1 != (c = getopt(argc, argv, "F:r:e:i:u:p:tcgh"))) {
+	while (-1 != (c = getopt(argc, argv, "T:r:e:i:u:p:tcgh"))) {
 		switch(c) {
-		case 'F':
+
+		case 'T':
 			im_truth = true;
-			sprintf(image_truth_fname, "%s", optarg);
+			image_truth_fname = strdup(optarg);
+			assert(NULL != image_truth_fname);
 			break;
 
 		case 'r':
@@ -292,6 +294,12 @@ int main(int argc, char* argv[])
 	unmap_cfl(N, ksp_dims, kspace_data);
 	unmap_cfl(N, img_dims, image);
 
+	if (im_truth) {
+
+		free((void*)image_truth_fname);
+		unmap_cfl(DIMS, img_dims, image_truth);
+	}
+
 	double end_time = timestamp();
 	debug_printf(DP_INFO, "Total Time: %f\n", end_time - start_time);
 

src/caldir.c

@@ -36,20 +36,20 @@ int main_caldir(int argc, char* argv[])
 {
 	mini_cmdline(argc, argv, 3, usage_str, help_str);
 
-	long dims[KSPACE_DIMS];
+	long dims[DIMS];
 
-	complex float* in_data = load_cfl(argv[2], KSPACE_DIMS, dims);
+	complex float* in_data = load_cfl(argv[2], DIMS, dims);
 
 	int calsize_ro = atoi(argv[1]);
 	long calsize[3] = { calsize_ro, calsize_ro, calsize_ro };
 
 	assert((dims[0] == 1) || (calsize_ro < dims[0]));
 	assert(1 == dims[4]);
 
-	complex float* out_data = create_cfl(argv[3], KSPACE_DIMS, dims);
+	complex float* out_data = create_cfl(argv[3], DIMS, dims);
 
 
-	long caldims[KSPACE_DIMS];
+	long caldims[DIMS];
 	complex float* cal_data = extract_calib(caldims, calsize, dims, in_data, false);
 
 	printf("Calibration region %ldx%ldx%ld\n", caldims[0], caldims[1], caldims[2]);
@@ -60,8 +60,8 @@ int main_caldir(int argc, char* argv[])
 
 	md_free(cal_data);
 
-	unmap_cfl(KSPACE_DIMS, dims, (void*)out_data);
-	unmap_cfl(KSPACE_DIMS, dims, (void*)in_data);
+	unmap_cfl(DIMS, dims, (void*)out_data);
+	unmap_cfl(DIMS, dims, (void*)in_data);
 
 	exit(0);
 }

src/calib/calib.c

@@ -64,6 +64,10 @@ static void eigen_herm3(int M, int N, float val[M], complex float matrix[N][N])
 
 
 
+/*
+ * rotate phase jointly along dim so that the 0-th slice along dim has phase = 0
+ *
+ */
 void fixphase(unsigned int N, const long dims[N], unsigned int dim, complex float* out, const complex float* in)
 {
 	assert(dim < N);