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Merged
yayahjb merged 2 commits into from
Sep 4, 2025
Merged

Avoid variable-length arrays #96

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5bb9365
Use CBF_START_ARRAY() and CBF_END_ARRAY() from cbf_alloc.h instead of…
hattne Jun 30, 2025
e6a1a06
Add roi_peaksearch to CMake build
hattne Jun 30, 2025
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7 changes: 7 additions & 0 deletions CMakeLists.txt
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Expand Up @@ -1152,6 +1152,13 @@ add_executable(testcell
target_link_libraries(testcell
cbf)

add_executable(roi_peaksearch
"${CBF__EXAMPLES}/dps_peaksearch.c"
"${CBF__EXAMPLES}/roi_peaksearch.c")
target_link_libraries(roi_peaksearch
cbf
"${libm}")

add_executable(sauter_test
"${CBF__EXAMPLES}/sauter_test.C")
target_link_libraries(sauter_test
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -2216,7 +2216,7 @@ $(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2ad
$(BIN)/cbf_standardize_numbers: $(EXAMPLES)/cbf_standardize_numbers.c $(EXAMPLES)/cbf_standardize_numbers.h
mkdir -p $(BIN)
$(CC) $(CFLAGS) $(LDFLAGS) $(MISCFLAG) $(CBF_REGEXFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) -L$(LIB) -lcbf $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@

#
# changtestcompression example program
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2 changes: 1 addition & 1 deletion Makefile_LINUX
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Expand Up @@ -2212,7 +2212,7 @@ $(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2ad
$(BIN)/cbf_standardize_numbers: $(EXAMPLES)/cbf_standardize_numbers.c $(EXAMPLES)/cbf_standardize_numbers.h
mkdir -p $(BIN)
$(CC) $(CFLAGS) $(LDFLAGS) $(MISCFLAG) $(CBF_REGEXFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) -L$(LIB) -lcbf $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@

#
# changtestcompression example program
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2 changes: 1 addition & 1 deletion Makefile_MINGW
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Expand Up @@ -2226,7 +2226,7 @@ $(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2ad
$(BIN)/cbf_standardize_numbers: $(EXAMPLES)/cbf_standardize_numbers.c $(EXAMPLES)/cbf_standardize_numbers.h
mkdir -p $(BIN)
$(CC) $(CFLAGS) $(LDFLAGS) $(MISCFLAG) $(CBF_REGEXFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) -L$(LIB) -lcbf $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@

#
# changtestcompression example program
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2 changes: 1 addition & 1 deletion Makefile_MSYS2
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Expand Up @@ -2211,7 +2211,7 @@ $(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2ad
$(BIN)/cbf_standardize_numbers: $(EXAMPLES)/cbf_standardize_numbers.c $(EXAMPLES)/cbf_standardize_numbers.h
mkdir -p $(BIN)
$(CC) $(CFLAGS) $(LDFLAGS) $(MISCFLAG) $(CBF_REGEXFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) -L$(LIB) -lcbf $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@

#
# changtestcompression example program
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2 changes: 1 addition & 1 deletion Makefile_OSX
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Expand Up @@ -2210,7 +2210,7 @@ $(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2ad
$(BIN)/cbf_standardize_numbers: $(EXAMPLES)/cbf_standardize_numbers.c $(EXAMPLES)/cbf_standardize_numbers.h
mkdir -p $(BIN)
$(CC) $(CFLAGS) $(LDFLAGS) $(MISCFLAG) $(CBF_REGEXFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) -L$(LIB) -lcbf $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@

#
# changtestcompression example program
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14 changes: 10 additions & 4 deletions examples/adscimg2cbf.c
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Expand Up @@ -12,6 +12,7 @@
#include <stdlib.h>
#include <string.h>
#include "cbf.h"
#include "cbf_alloc.h"
#include "cbf_string.h"

/****************************************************************/
Expand Down Expand Up @@ -155,8 +156,7 @@ int main(int argc, char *argv[])
char header_bytes[6];
int numargs = argc;
int iarg;
int argtype_array[argc];
int *argtype=argtype_array;
int *argtype;
int filec;
int file_size, header_size_char, actread;
int cbf_status;
Expand All @@ -174,8 +174,7 @@ int main(int argc, char *argv[])
int *new_int_data, *old_int_data;
size_t new_int_data_size, old_int_data_size;
double thickness=0.;
const char * argval_array[argc];
const char * * argval=argval_array;
const char * * argval;
const char * roi=NULL;
const char * thickstr=NULL;
const char * polarstr=NULL;
Expand Down Expand Up @@ -232,6 +231,11 @@ int main(int argc, char *argv[])
CBF_UNUSED( cbf_status );
CBF_UNUSED( thickness );

CBF_START_ARRAY(int, argtype_array, argc);
argtype = argtype_array;
CBF_START_ARRAY(const char *, argval_array, argc);
argval = argval_array;

if(argc < 2)
{
usage();
Expand Down Expand Up @@ -641,5 +645,7 @@ int main(int argc, char *argv[])
filec--;
}
}
CBF_END_ARRAY(argval_array);
CBF_END_ARRAY(argtype_array);
exit(0);
}
4 changes: 3 additions & 1 deletion examples/cbf_standardize_numbers.c
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Expand Up @@ -7,6 +7,7 @@
//

#include "cbf.h"
#include "cbf_alloc.h"
#include "cbf_standardize_numbers.h"
#include <stdio.h>
#include <stdlib.h>
Expand Down Expand Up @@ -107,7 +108,7 @@ int main (int argc, char ** argv) {
continue;
}
if (isdigit(c) || c == '.' || c == '-' || c == '+') {
char text[lineln+1];
CBF_START_ARRAY(char, text, lineln+1);
char * endptr;
for (ii=0; ii < lineln; ii++) text[ii] = line[ii];
text[lineln] = '\0';
Expand Down Expand Up @@ -139,6 +140,7 @@ int main (int argc, char ** argv) {
spacestarted = 1;
numcomp++;
}
CBF_END_ARRAY(text);
continue;
}
if (c == ',' || (termc && c == termc)) {
Expand Down
48 changes: 28 additions & 20 deletions examples/dps_peaksearch.c
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Expand Up @@ -69,6 +69,8 @@
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "cbf.h"
#include "cbf_alloc.h"
#include "dps_peaksearch.h"


Expand All @@ -82,14 +84,13 @@ int xirint(double x) {
}


#if defined (__linux__)||defined(sun)
#if defined(sun)
/* Round a double to an integer */


/* Calculate sin() and cos(). */
void
sincos(x, s, c)
double x, *s, *c;
static void
sincos(double x, double *s, double *c)
{
*s = sin(x);
*c = cos(x);
Expand All @@ -100,19 +101,17 @@ double x, *s, *c;


/* Calculate sin() and cos(). */
void
sincos(x, s, c)
double x, *s, *c;
static void
sincos(double x, double *s, double *c)
{
*s = sin(x);
*c = cos(x);
}


/* Round a double to an integer */
double
rint(x)
register double x;
static double
rint(register double x)
{
if (x == (int)x)
return(x);
Expand All @@ -137,12 +136,16 @@ int fsign(double x)
*
*/

void
cmass (idata, iwidth, iheight, x, y, cm_x, cm_y, cm_nx, cm_ny)
register unsigned short *idata;
int iwidth, iheight, x, y;
double *cm_x, *cm_y;
int cm_nx, cm_ny;
static void
cmass(register unsigned short *idata,
int iwidth,
int iheight,
int x,
int y,
double *cm_x,
double *cm_y,
int cm_nx,
int cm_ny)
{
register int i, j, val;
double sum_x=0, sum_y=0, sum_z=0.0;
Expand Down Expand Up @@ -203,6 +206,9 @@ static DPS_Peak *dps_peaks = NULL;

static int ccd_image_saturation = 0;

int
sortfunc(const void *lhs, const void *rhs);

int dps_peaksearch(unsigned short *data, int nx, int ny,
int npeaks_out, double min_isigma,
int min_spacing, DPS_Peak *pptr, int min_value)
Expand All @@ -229,13 +235,11 @@ int dps_peaksearch(unsigned short *data, int nx, int ny,
int overload = 55000;
int npeaks=0;
int maxpeaks=20480;
int sortfunc();
int nover;
int nunder;
int nxfer;
DPS_Peak dps_temp;
int peakfw, peakfh;
int next_good_y[nx];
int collide;

stepx = (min_spacing+1)/2; /* Initial stepsize for scanning through the image */
Expand Down Expand Up @@ -267,6 +271,7 @@ int dps_peaksearch(unsigned short *data, int nx, int ny,
}

/* Initialize the next_good_y array to 0 */
CBF_START_ARRAY(int, next_good_y, nx);
for (i=0; i < nx; i++) next_good_y[i]= 0;

/* The next two loops go over the whole frame with stepsize
Expand Down Expand Up @@ -444,6 +449,7 @@ int dps_peaksearch(unsigned short *data, int nx, int ny,
}
}
}
CBF_END_ARRAY(next_good_y);

if (min_spacing > 0) {
for(i=0;i<npeaks;i++)
Expand Down Expand Up @@ -485,9 +491,11 @@ int dps_peaksearch(unsigned short *data, int nx, int ny,
/* Sort pixel value
*/
int
sortfunc(pk1, pk2)
DPS_Peak *pk1, *pk2;
sortfunc(const void *lhs, const void *rhs)
{
const DPS_Peak *pk1 = lhs;
const DPS_Peak *pk2 = rhs;

if (pk2->isigma > pk1->isigma)
return 1;
else
Expand Down
9 changes: 7 additions & 2 deletions examples/testhdf5.c
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Expand Up @@ -53,6 +53,7 @@
#include <stdint.h>

#include "cbf.h"
#include "cbf_alloc.h"
#include "cbf_hdf5.h"
#include "unittest.h"

Expand Down Expand Up @@ -901,8 +902,6 @@ static testResult_t testDataset_read_write(const hid_t grp)
const int N2 = N*2;
int dataWrite0[] = {42};
int dataRead0[] = {0};
int dataWrite2[N2];
int dataRead2[N2];
const int rank = 2;
const hsize_t offset[] = {0,0};
const hsize_t offset_1[] = {1,0};
Expand All @@ -915,6 +914,9 @@ static testResult_t testDataset_read_write(const hid_t grp)
const hsize_t chunk[] = {1,N2};
TEST(H5I_GROUP==H5Iget_type(grp));

CBF_START_ARRAY(int, dataWrite2, N2);
CBF_START_ARRAY(int, dataRead2, N2);

{/* populate the data */
int i;
for (i = 0; i < N2; ++i) dataWrite2[i] = i*i;
Expand Down Expand Up @@ -1035,6 +1037,9 @@ static testResult_t testDataset_read_write(const hid_t grp)
if (CBF_SUCCESS!=error)
fprintf(stderr,"%s: Error: %s\n",__WHERE__,cbf_strerror(error));

CBF_END_ARRAY(dataRead2);
CBF_END_ARRAY(dataWrite2);

/* free the handle after using it */
cbf_H5Dfree(handle0);
cbf_H5Dfree(handle2);
Expand Down
2 changes: 1 addition & 1 deletion m4/Makefile.m4
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Expand Up @@ -2585,7 +2585,7 @@ $(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2ad
$(BIN)/cbf_standardize_numbers: $(EXAMPLES)/cbf_standardize_numbers.c $(EXAMPLES)/cbf_standardize_numbers.h
mkdir -p $(BIN)
$(CC) $(CFLAGS) $(LDFLAGS) $(MISCFLAG) $(CBF_REGEXFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@
$(EXAMPLES)/cbf_standardize_numbers.c $(SRC_FGETLN) -L$(LIB) -lcbf $(REGEX_LIBS_STATIC) $(EXTRALIBS) -o $@

#
# changtestcompression example program
Expand Down
17 changes: 12 additions & 5 deletions src/cbf_hdf5.c
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Expand Up @@ -11839,7 +11839,7 @@ _cbf_pilatusAxis2nexusAxisAttrs(h4data,units,depends_on,exsisItem,cmp)

size_t ii, rank, adim;

double oldvec[dimension];
CBF_START_ARRAY(double, oldvec, dimension);

CBF_UNUSED( adim );

Expand Down Expand Up @@ -11880,6 +11880,8 @@ _cbf_pilatusAxis2nexusAxisAttrs(h4data,units,depends_on,exsisItem,cmp)

if (cbf_H5Ivalid(attribid)) H5Aclose(attribid);

CBF_END_ARRAY(oldvec);

return errorcode;

}
Expand Down Expand Up @@ -22090,7 +22092,7 @@ _cbf_pilatusAxis2nexusAxisAttrs(h4data,units,depends_on,exsisItem,cmp)
cbf_debug_print("error: problem getting the rank of a dataset");
error |= CBF_H5ERROR;
} else if (rank > 0) {
hsize_t dims[rank];
CBF_START_ARRAY(hsize_t, dims, rank);
if (rank != H5Sget_simple_extent_dims(data_space,dims,0)) {
cbf_debug_print("error: problem getting the dimensions of a dataset");
error |= CBF_H5ERROR;
Expand All @@ -22105,8 +22107,8 @@ _cbf_pilatusAxis2nexusAxisAttrs(h4data,units,depends_on,exsisItem,cmp)
- assume that it's a uniformly spaced array of pixels in 3D space, so ignore subsequent values
- store it (and dependency chain) in the key, to be converted along with other axes
*/
hsize_t off[rank];
hsize_t cnt[rank];
CBF_START_ARRAY(hsize_t, off, rank);
CBF_START_ARRAY(hsize_t, cnt, rank);
size_t ir;
double disp2[] = {0.,0.};
double factor = 0./0.;
Expand Down Expand Up @@ -22140,7 +22142,10 @@ _cbf_pilatusAxis2nexusAxisAttrs(h4data,units,depends_on,exsisItem,cmp)
free((void*)long_name_string);
cbf_H5Afree(long_name);
}
CBF_END_ARRAY(cnt);
CBF_END_ARRAY(off);
}
CBF_END_ARRAY(dims);
} else {
cbf_debug_print("error: unsupported rank of a 'pixel_offset' field");
error |= CBF_NOTIMPLEMENTED;
Expand Down Expand Up @@ -28873,7 +28878,7 @@ CBF_CALL(CBFM_pilatusAxis2nexusAxisAttrs(h5data,token,"",axisItem,cmp_double,cmp

if (type_class==H5T_STRING) {

char element[type_size+1];
CBF_START_ARRAY(char, element, type_size+1);

size_t ii, jj;;

Expand Down Expand Up @@ -28903,6 +28908,8 @@ CBF_CALL(CBFM_pilatusAxis2nexusAxisAttrs(h5data,token,"",axisItem,cmp_double,cmp

}

CBF_END_ARRAY(element);

} else if (type_class==H5T_INTEGER){

/* Read of a single integer or an integer array of
Expand Down
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