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authorThomas White <taw@physics.org>2015-02-20 14:51:17 +0100
committerThomas White <taw@physics.org>2015-02-20 14:51:17 +0100
commita388a84d3377812332194c134e404c94d20c7706 (patch)
tree1c0631ef8ea7e1b704db042c6d826f096fddec4d /libcrystfel
parent6ad20e4d35878c7fccc5bf765c2f33f1117e3c4d (diff)
Rationalise get_value() stuff
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/detector.c12
-rw-r--r--libcrystfel/src/hdf5-file.c480
-rw-r--r--libcrystfel/src/hdf5-file.h7
3 files changed, 229 insertions, 270 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 4f58df9c..635aa5e2 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -565,11 +565,15 @@ void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev)
if ( p->clen_from != NULL ) {
- if (det->path_dim !=0 || det->dim_dim !=0 ){
- p->clen = get_ev_based_value(f, p->clen_from,
- ev) * 1.0e-3;
+ double val;
+ int r;
+
+ r = get_value(f, p->clen_from, ev, &val,
+ H5T_NATIVE_DOUBLE);
+ if ( r ) {
+ ERROR("Failed to read '%s'\n", p->clen_from);
} else {
- p->clen = get_value(f, p->clen_from) * 1.0e-3;
+ p->clen = val * 1.0e-3;
}
}
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 25e700ab..5f34a3c8 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -1151,6 +1151,201 @@ static int unpack_panels(struct image *image, struct detector *det)
}
+static int get_scalar_value(struct hdfile *f, const char *name, void *val,
+ hid_t memtype)
+{
+ hid_t dh;
+ hid_t type;
+ hid_t class;
+ herr_t r;
+ int check;
+
+ if ( !hdfile_is_scalar(f, name, 1) ) return 1;
+
+ check = check_path_existence(f->fh, name);
+ if ( check == 0 ) {
+ ERROR("No such float field '%s'\n", name);
+ return 1;
+ }
+
+ dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
+
+ type = H5Dget_type(dh);
+ class = H5Tget_class(type);
+
+ if ( class != H5T_FLOAT ) {
+ ERROR("Not a floating point value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+
+ r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, val);
+ if ( r < 0 ) {
+ ERROR("Couldn't read value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+
+ return 0;
+}
+
+
+static int get_ev_based_value(struct hdfile *f, const char *name,
+ struct event *ev, void *val, hid_t memtype)
+{
+ hid_t dh;
+ hid_t type;
+ hid_t class;
+ hid_t sh;
+ hid_t ms;
+ hsize_t *f_offset = NULL;
+ hsize_t *f_count = NULL;
+ hsize_t m_offset[1];
+ hsize_t m_count[1];
+ hsize_t msdims[1];
+ hsize_t size[3];
+ herr_t r;
+ herr_t check;
+ int check_pe;
+ int dim_flag;
+ int ndims;
+ int i;
+ char *subst_name = NULL;
+
+ if ( ev->path_length != 0 ) {
+ subst_name = partial_event_substitution(ev, name);
+ } else {
+ subst_name = strdup(name);
+ }
+
+ check_pe = check_path_existence(f->fh, subst_name);
+ if ( check_pe == 0 ) {
+ ERROR("No such event-based float field '%s'\n", subst_name);
+ return 1;
+ }
+
+ dh = H5Dopen2(f->fh, subst_name, H5P_DEFAULT);
+ type = H5Dget_type(dh);
+ class = H5Tget_class(type);
+
+ if ( class != H5T_FLOAT ) {
+ ERROR("Not a floating point value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+
+ /* Get the dimensionality. We have to cope with scalars expressed as
+ * arrays with all dimensions 1, as well as zero-d arrays. */
+ sh = H5Dget_space(dh);
+ ndims = H5Sget_simple_extent_ndims(sh);
+ if ( ndims > 3 ) {
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+ H5Sget_simple_extent_dims(sh, size, NULL);
+
+ m_offset[0] = 0;
+ m_count[0] = 1;
+ msdims[0] = 1;
+ ms = H5Screate_simple(1,msdims,NULL);
+
+ /* Check that the size in all dimensions is 1 */
+ /* or that one of the dimensions has the same */
+ /* size as the hyperplane events */
+
+ dim_flag = 0;
+
+ for ( i=0; i<ndims; i++ ) {
+ if ( size[i] != 1 ) {
+ if ( i == 0 && size[i] > ev->dim_entries[0] ) {
+ dim_flag = 1;
+ } else {
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+ }
+ }
+
+ if ( dim_flag == 0 ) {
+
+ r = H5Dread(dh, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, val);
+
+ if ( r < 0 ) {
+ ERROR("Couldn't read value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+
+ } else {
+
+ f_offset = malloc(ndims*sizeof(hsize_t));
+ f_count = malloc(ndims*sizeof(hsize_t));
+
+ for ( i=0; i<ndims; i++ ) {
+
+ if ( i == 0 ) {
+ f_offset[i] = ev->dim_entries[0];
+ f_count[i] = 1;
+ } else {
+ f_offset[i] = 0;
+ f_count[i] = 0;
+ }
+
+ }
+
+ check = H5Sselect_hyperslab(sh, H5S_SELECT_SET,
+ f_offset, NULL, f_count, NULL);
+ if ( check <0 ) {
+ ERROR("Error selecting dataspace for float value");
+ free(f_offset);
+ free(f_count);
+ return 1;
+ }
+
+ ms = H5Screate_simple(1,msdims,NULL);
+ check = H5Sselect_hyperslab(ms, H5S_SELECT_SET,
+ m_offset, NULL, m_count, NULL);
+ if ( check < 0 ) {
+ ERROR("Error selecting memory dataspace for float value");
+ free(f_offset);
+ free(f_count);
+ return 1;
+ }
+
+ r = H5Dread(dh, memtype, ms, sh, H5P_DEFAULT, val);
+ if ( r < 0 ) {
+ ERROR("Couldn't read value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return 1;
+ }
+
+ }
+
+ free(subst_name);
+
+ return 0;
+}
+
+
+int get_value(struct hdfile *f, const char *name,
+ struct event *ev, void *val, hid_t memtype)
+{
+ if ( ev == NULL ) {
+ return get_scalar_value(f, name, val, memtype);
+ } else {
+ return get_ev_based_value(f, name, ev, val, memtype);
+ }
+}
+
+
void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
struct event *ev, struct image *image)
{
@@ -1161,15 +1356,16 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
/* Explicit value given */
eV = beam->photon_energy;
- } else if ( ev != NULL ) {
-
- /* Value from HDF5 file, event-based structure */
- eV = get_ev_based_value(f, beam->photon_energy_from, ev);
-
} else {
- /* Value from HDF5 file, single-event structure */
- eV = get_value(f, beam->photon_energy_from);
+ int r;
+
+ r = get_value(f, beam->photon_energy_from, ev, &eV,
+ H5T_NATIVE_DOUBLE);
+ if ( r ) {
+ ERROR("Failed to read '%s'\n",
+ beam->photon_energy_from);
+ }
}
@@ -1589,255 +1785,6 @@ int hdfile_is_scalar(struct hdfile *f, const char *name, int verbose)
}
-
-
-static int get_f_value(struct hdfile *f, const char *name, double *val)
-{
- hid_t dh;
- hid_t type;
- hid_t class;
- herr_t r;
- double buf;
- int check;
-
- if ( !hdfile_is_scalar(f, name, 1) ) return 1;
-
- check = check_path_existence(f->fh, name);
- if ( check == 0 ) {
- ERROR("No such float field '%s'\n", name);
- return 1;
- }
-
- dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
-
- type = H5Dget_type(dh);
- class = H5Tget_class(type);
-
- if ( class != H5T_FLOAT ) {
- ERROR("Not a floating point value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, &buf);
- if ( r < 0 ) {
- ERROR("Couldn't read value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- *val = buf;
- return 0;
-}
-
-
-static int get_ev_based_f_value(struct hdfile *f, const char *name,
- struct event *ev, double *val)
-{
- hid_t dh;
- hid_t type;
- hid_t class;
- hid_t sh;
- hid_t ms;
- hsize_t *f_offset = NULL;
- hsize_t *f_count = NULL;
- hsize_t m_offset[1];
- hsize_t m_count[1];
- hsize_t msdims[1];
- hsize_t size[3];
- herr_t r;
- herr_t check;
- double buf;
- int check_pe;
- int dim_flag;
- int ndims;
- int i;
- char *subst_name = NULL;
-
- if ( ev->path_length != 0 ) {
- subst_name = partial_event_substitution(ev, name);
- } else {
- subst_name = strdup(name);
- }
-
- check_pe = check_path_existence(f->fh, subst_name);
- if ( check_pe == 0 ) {
- ERROR("No such event-based float field '%s'\n", subst_name);
- return 1;
- }
-
- dh = H5Dopen2(f->fh, subst_name, H5P_DEFAULT);
- type = H5Dget_type(dh);
- class = H5Tget_class(type);
-
- if ( class != H5T_FLOAT ) {
- ERROR("Not a floating point value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- /* Get the dimensionality. We have to cope with scalars expressed as
- * arrays with all dimensions 1, as well as zero-d arrays. */
- sh = H5Dget_space(dh);
- ndims = H5Sget_simple_extent_ndims(sh);
- if ( ndims > 3 ) {
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
- H5Sget_simple_extent_dims(sh, size, NULL);
-
- m_offset[0] = 0;
- m_count[0] = 1;
- msdims[0] = 1;
- ms = H5Screate_simple(1,msdims,NULL);
-
- /* Check that the size in all dimensions is 1 */
- /* or that one of the dimensions has the same */
- /* size as the hyperplane events */
-
- dim_flag = 0;
-
- for ( i=0; i<ndims; i++ ) {
- if ( size[i] != 1 ) {
- if ( i == 0 && size[i] > ev->dim_entries[0] ) {
- dim_flag = 1;
- } else {
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
- }
- }
-
- if ( dim_flag == 0 ) {
-
- r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, &buf);
-
- if ( r < 0 ) {
- ERROR("Couldn't read value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- } else {
-
- f_offset = malloc(ndims*sizeof(hsize_t));
- f_count = malloc(ndims*sizeof(hsize_t));
-
- for ( i=0; i<ndims; i++ ) {
-
- if ( i == 0 ) {
- f_offset[i] = ev->dim_entries[0];
- f_count[i] = 1;
- } else {
- f_offset[i] = 0;
- f_count[i] = 0;
- }
-
- }
-
- check = H5Sselect_hyperslab(sh, H5S_SELECT_SET,
- f_offset, NULL, f_count, NULL);
- if ( check <0 ) {
- ERROR("Error selecting dataspace for float value");
- free(f_offset);
- free(f_count);
- return 1;
- }
-
- ms = H5Screate_simple(1,msdims,NULL);
- check = H5Sselect_hyperslab(ms, H5S_SELECT_SET,
- m_offset, NULL, m_count, NULL);
- if ( check < 0 ) {
- ERROR("Error selecting memory dataspace for float value");
- free(f_offset);
- free(f_count);
- return 1;
- }
-
- r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh,
- H5P_DEFAULT, &buf);
- if ( r < 0 ) {
- ERROR("Couldn't read value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- }
-
- free(subst_name);
- *val = buf;
-
- return 0;
-}
-
-
-static int get_i_value(struct hdfile *f, const char *name, int *val)
-{
- hid_t dh;
- hid_t type;
- hid_t class;
- herr_t r;
- int buf;
- int check;
-
- if ( !hdfile_is_scalar(f, name, 1) ) return 1;
-
- check = check_path_existence(f->fh, name);
- if ( check == 0 ) {
- ERROR("No such integer field '%s'\n", name);
- return 1;
- }
-
- dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
- type = H5Dget_type(dh);
- class = H5Tget_class(type);
-
- if ( class != H5T_INTEGER ) {
- ERROR("Not an integer value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- r = H5Dread(dh, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, &buf);
- if ( r < 0 ) {
- ERROR("Couldn't read value.\n");
- H5Tclose(type);
- H5Dclose(dh);
- return 1;
- }
-
- *val = buf;
- return 0;
-}
-
-
-double get_value(struct hdfile *f, const char *name)
-{
- double val = 0.0;
- get_f_value(f, name, &val);
- return val;
-}
-
-double get_ev_based_value(struct hdfile *f, const char *name,
- struct event *ev)
-{
- double val = -1;
- get_ev_based_f_value(f, name, ev, &val);
- return val;
-}
-
-
struct copy_hdf5_field
{
char **fields;
@@ -1986,17 +1933,26 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name,
}
} else {
+ int r;
+
switch ( class ) {
+
case H5T_FLOAT :
- if ( get_f_value(f, subst_name, &buf_f) ) break;
- tmp = malloc(256);
- snprintf(tmp, 255, "%f", buf_f);
+ r = get_value(f, subst_name, ev, &buf_f,
+ H5T_NATIVE_DOUBLE);
+ if ( r == 0 ) {
+ tmp = malloc(256);
+ snprintf(tmp, 255, "%f", buf_f);
+ }
break;
case H5T_INTEGER :
- if ( get_i_value(f, subst_name, &buf_i) ) break;
- tmp = malloc(256);
- snprintf(tmp, 255, "%d", buf_i);
+ r = get_value(f, subst_name, ev, &buf_i,
+ H5T_NATIVE_INT);
+ if ( r == 0 ) {
+ tmp = malloc(256);
+ snprintf(tmp, 255, "%d", buf_i);
+ }
break;
}
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index 2988b929..721c1eea 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -83,10 +83,6 @@ extern int get_peaks(struct image *image, struct hdfile *f, const char *p);
extern int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p,
struct filename_plus_event *fpe);
-extern double get_value(struct hdfile *f, const char *name);
-
-extern double get_ev_based_value(struct hdfile *f, const char *name,
- struct event *ev);
extern struct copy_hdf5_field *new_copy_hdf5_field_list(void);
extern void free_copy_hdf5_field_list(struct copy_hdf5_field *f);
@@ -99,6 +95,9 @@ extern void add_copy_hdf5_field(struct copy_hdf5_field *copyme,
extern struct event_list *fill_event_list(struct hdfile* hdfile,
struct detector* det);
+extern int get_value(struct hdfile *f, const char *name,
+ struct event *ev, void *val, hid_t memtype);
+
#ifdef __cplusplus
}
#endif