[cig-commits] r5422 - mc/3D/CitcomS/trunk/visual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Dec 1 20:43:50 PST 2006
Author: tan2
Date: 2006-12-01 20:43:50 -0800 (Fri, 01 Dec 2006)
New Revision: 5422
Added:
mc/3D/CitcomS/trunk/visual/h5util.c
mc/3D/CitcomS/trunk/visual/h5util.h
Modified:
mc/3D/CitcomS/trunk/visual/Makefile.am
mc/3D/CitcomS/trunk/visual/h5tovelo.c
Log:
Moved utility functions to h5util.c
Modified: mc/3D/CitcomS/trunk/visual/Makefile.am
===================================================================
--- mc/3D/CitcomS/trunk/visual/Makefile.am 2006-12-02 04:15:26 UTC (rev 5421)
+++ mc/3D/CitcomS/trunk/visual/Makefile.am 2006-12-02 04:43:50 UTC (rev 5422)
@@ -117,8 +117,8 @@
if COND_HDF5
bin_PROGRAMS = h5tocap h5tovelo
- h5tocap_SOURCES = h5tocap.c
- h5tovelo_SOURCES = h5tovelo.c
+ h5tocap_SOURCES = h5tocap.c h5util.c
+ h5tovelo_SOURCES = h5tovelo.c h5util.c
h5tovelo_LDADD = $(LIBHDF5)
endif
Modified: mc/3D/CitcomS/trunk/visual/h5tovelo.c
===================================================================
--- mc/3D/CitcomS/trunk/visual/h5tovelo.c 2006-12-02 04:15:26 UTC (rev 5421)
+++ mc/3D/CitcomS/trunk/visual/h5tovelo.c 2006-12-02 04:43:50 UTC (rev 5422)
@@ -20,6 +20,7 @@
#include <stdio.h>
#include <stdlib.h>
#include "hdf5.h"
+#include "h5util.h"
static const char usage[] =
@@ -31,34 +32,7 @@
"step: time step\n";
-typedef struct field_t
-{
- const char *name;
- int rank;
- hsize_t *dims;
- hsize_t *maxdims;
-
- hsize_t *offset;
- hsize_t *count;
-
- int n;
- float *data;
-
-} field_t;
-
-
-static field_t *open_field(hid_t cap, const char *name);
-static herr_t read_field(hid_t cap, field_t *field, int iii);
-static herr_t close_field(field_t *field);
-
-static herr_t get_attribute_str(hid_t obj_id, const char *attr_name, char **data);
-static herr_t get_attribute_int(hid_t input, const char *name, int *val);
-static herr_t get_attribute_float(hid_t input, const char *name, float *val);
-static herr_t get_attribute(hid_t obj_id, const char *attr_name, hid_t mem_type_id, void *data);
-static herr_t get_attribute_mem(hid_t obj_id, const char *attr_name, hid_t mem_type_id, void *data);
-
-
int main(int argc, char *argv[])
{
char filename1[100];
@@ -232,330 +206,3 @@
return 0;
}
-
-
-static field_t *open_field(hid_t file_id, const char *name)
-{
- hid_t dataset;
- hid_t dataspace;
- herr_t status;
-
- int d;
- int rank;
-
- field_t *field;
-
- if (file_id < 0)
- return NULL;
-
-
- /* Allocate field and initialize. */
-
- field = (field_t *)malloc(sizeof(field_t));
-
- field->name = name;
- field->rank = 0;
- field->dims = NULL;
- field->maxdims = NULL;
- field->n = 0;
-
- dataset = H5Dopen(file_id, name);
- if(dataset < 0)
- {
- free(field);
- fprintf(stderr, "Could not open HDF5 dataset \"%s\"\n", name);
- return NULL;
- }
-
- dataspace = H5Dget_space(dataset);
- if (dataspace < 0)
- {
- free(field);
- fprintf(stderr, "Could not open HDF5 dataspace \"%s\"\n", name);
- return NULL;
- }
-
-
- /* Calculate shape of field. */
-
- rank = H5Sget_simple_extent_ndims(dataspace);
-
- field->rank = rank;
- field->dims = (hsize_t *)malloc(rank * sizeof(hsize_t));
- field->maxdims = (hsize_t *)malloc(rank * sizeof(hsize_t));
-
- status = H5Sget_simple_extent_dims(dataspace, field->dims, field->maxdims);
-
- /* DEBUG
- printf("Field %s shape (", name);
- for(d = 0; d < rank; d++)
- printf("%d,", (int)(field->dims[d]));
- printf(")\n");
- // */
-
-
- /* Allocate memory for hyperslab selection parameters. */
-
- field->offset = (hsize_t *)malloc(rank * sizeof(hsize_t));
- field->count = (hsize_t *)malloc(rank * sizeof(hsize_t));
-
-
- /* Allocate enough memory for a single cap-slice buffer. */
-
- field->n = 1;
- for(d = 1; d < rank; d++)
- field->n *= field->dims[d];
-
- field->data = (float *)malloc(field->n * sizeof(float));
-
-
- /* Release resources. */
-
- status = H5Sclose(dataspace);
- status = H5Dclose(dataset);
-
- return field;
-}
-
-
-static herr_t read_field(hid_t file_id, field_t *field, int iii)
-{
- hid_t dataset;
- hid_t filespace;
- hid_t memspace;
- herr_t status;
-
- int d;
-
- if (file_id < 0 || field == NULL)
- return -1;
-
- dataset = H5Dopen(file_id, field->name);
-
- if (dataset < 0)
- return -1;
-
- field->offset[0] = iii;
- field->count[0] = 1;
- for(d = 1; d < field->rank; d++)
- {
- field->offset[d] = 0;
- field->count[d] = field->dims[d];
- }
-
-
- /* DEBUG */
- printf("Reading cap %d on field %s with offset (", iii, field->name);
- for(d = 0; d < field->rank; d++) printf("%d,", (int)(field->offset[d]));
- printf(") and count (");
- for(d = 0; d < field->rank; d++) printf("%d,", (int)(field->count[d]));
- printf(")\n");
- // */
-
-
- filespace = H5Dget_space(dataset);
-
- status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET,
- field->offset, NULL, field->count, NULL);
-
- memspace = H5Screate_simple(field->rank, field->count, NULL);
-
- status = H5Dread(dataset, H5T_NATIVE_FLOAT, memspace,
- filespace, H5P_DEFAULT, field->data);
-
- status = H5Sclose(filespace);
- status = H5Sclose(memspace);
- status = H5Dclose(dataset);
-
- return 0;
-}
-
-
-static herr_t close_field(field_t *field)
-{
- if (field != NULL)
- {
- free(field->dims);
- free(field->maxdims);
- free(field->offset);
- free(field->count);
- free(field->data);
- free(field);
- }
- return 0;
-}
-
-static herr_t get_attribute_str(hid_t obj_id,
- const char *attr_name,
- char **data)
-{
- hid_t attr_id;
- hid_t attr_type;
- size_t type_size;
- herr_t status;
-
- *data = NULL;
-
- attr_id = H5Aopen_name(obj_id, attr_name);
- if (attr_id < 0)
- return -1;
-
- attr_type = H5Aget_type(attr_id);
- if (attr_type < 0)
- goto out;
-
- /* Get the size */
- type_size = H5Tget_size(attr_type);
- if (type_size < 0)
- goto out;
-
- /* malloc enough space for the string, plus 1 for trailing '\0' */
- *data = (char *)malloc(type_size + 1);
-
- status = H5Aread(attr_id, attr_type, *data);
- if (status < 0)
- goto out;
-
- /* Set the last character to '\0' in case we are dealing with
- * null padded or space padded strings
- */
- (*data)[type_size] = '\0';
-
- status = H5Tclose(attr_type);
- if (status < 0)
- goto out;
-
- status = H5Aclose(attr_id);
- if (status < 0)
- return -1;
-
- return 0;
-
-out:
- H5Tclose(attr_type);
- H5Aclose(attr_id);
- if (*data)
- free(*data);
- return -1;
-}
-
-static herr_t get_attribute_int(hid_t input, const char *name, int *val)
-{
- hid_t attr_id;
- hid_t type_id;
- H5T_class_t type_class;
- size_t type_size;
-
- herr_t status;
-
- char *strval;
-
- attr_id = H5Aopen_name(input, name);
- type_id = H5Aget_type(attr_id);
- type_class = H5Tget_class(type_id);
- type_size = H5Tget_size(type_id);
-
- H5Tclose(type_id);
- H5Aclose(attr_id);
-
- switch(type_class)
- {
- case H5T_STRING:
- status = get_attribute_str(input, name, &strval);
- if (status < 0) return -1;
- *val = atoi(strval);
- free(strval);
- return 0;
- case H5T_INTEGER:
- status = get_attribute(input, name, H5T_NATIVE_INT, val);
- if (status < 0) return -1;
- return 0;
- default:
- return -1;
- }
-
- return -1;
-}
-
-
-static herr_t get_attribute_float(hid_t input, const char *name, float *val)
-{
- hid_t attr_id;
- hid_t type_id;
- H5T_class_t type_class;
- size_t type_size;
-
- herr_t status;
-
- char *strval;
-
- attr_id = H5Aopen_name(input, name);
- type_id = H5Aget_type(attr_id);
- type_class = H5Tget_class(type_id);
- type_size = H5Tget_size(type_id);
-
- H5Tclose(type_id);
- H5Aclose(attr_id);
-
- switch(type_class)
- {
- case H5T_STRING:
- status = get_attribute_str(input, name, &strval);
- if (status < 0) return -1;
- *val = atof(strval);
- free(strval);
- return 0;
- case H5T_FLOAT:
- status = get_attribute(input, name, H5T_NATIVE_FLOAT, val);
- if (status < 0) return -1;
- return 0;
- default:
- return -1;
- }
-
- return -1;
-}
-
-
-static herr_t get_attribute(hid_t obj_id,
- const char *attr_name,
- hid_t mem_type_id,
- void *data)
-{
- herr_t status;
-
- status = get_attribute_mem(obj_id, attr_name, mem_type_id, data);
- if (status < 0)
- return -1;
-
- return 0;
-}
-
-
-static herr_t get_attribute_mem(hid_t obj_id,
- const char *attr_name,
- hid_t mem_type_id,
- void *data)
-{
- hid_t attr_id;
- herr_t status;
-
- attr_id = H5Aopen_name(obj_id, attr_name);
- if (attr_id < 0)
- return -1;
-
- status = H5Aread(attr_id, mem_type_id, data);
- if (status < 0)
- {
- H5Aclose(attr_id);
- return -1;
- }
-
- status = H5Aclose(attr_id);
- if (status < 0)
- return -1;
-
- return 0;
-}
-
-
Added: mc/3D/CitcomS/trunk/visual/h5util.c
===================================================================
--- mc/3D/CitcomS/trunk/visual/h5util.c 2006-12-02 04:15:26 UTC (rev 5421)
+++ mc/3D/CitcomS/trunk/visual/h5util.c 2006-12-02 04:43:50 UTC (rev 5422)
@@ -0,0 +1,353 @@
+/*
+ * h5util.c by Luis Armendariz and Eh Tan.
+ * Copyright (C) 2006, California Institute of Technology.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "h5util.h"
+
+
+static herr_t get_attribute(hid_t obj_id, const char *attr_name, hid_t mem_type_id, void *data);
+static herr_t get_attribute_mem(hid_t obj_id, const char *attr_name, hid_t mem_type_id, void *data);
+
+
+field_t *open_field(hid_t file_id, const char *name)
+{
+ hid_t dataset;
+ hid_t dataspace;
+ herr_t status;
+
+ int d;
+ int rank;
+
+ field_t *field;
+
+ if (file_id < 0)
+ return NULL;
+
+
+ /* Allocate field and initialize. */
+
+ field = (field_t *)malloc(sizeof(field_t));
+
+ field->name = name;
+ field->rank = 0;
+ field->dims = NULL;
+ field->maxdims = NULL;
+ field->n = 0;
+
+ dataset = H5Dopen(file_id, name);
+ if(dataset < 0)
+ {
+ free(field);
+ fprintf(stderr, "Could not open HDF5 dataset \"%s\"\n", name);
+ return NULL;
+ }
+
+ dataspace = H5Dget_space(dataset);
+ if (dataspace < 0)
+ {
+ free(field);
+ fprintf(stderr, "Could not open HDF5 dataspace \"%s\"\n", name);
+ return NULL;
+ }
+
+
+ /* Calculate shape of field. */
+
+ rank = H5Sget_simple_extent_ndims(dataspace);
+
+ field->rank = rank;
+ field->dims = (hsize_t *)malloc(rank * sizeof(hsize_t));
+ field->maxdims = (hsize_t *)malloc(rank * sizeof(hsize_t));
+
+ status = H5Sget_simple_extent_dims(dataspace, field->dims, field->maxdims);
+
+ /* DEBUG
+ printf("Field %s shape (", name);
+ for(d = 0; d < rank; d++)
+ printf("%d,", (int)(field->dims[d]));
+ printf(")\n");
+ // */
+
+
+ /* Allocate memory for hyperslab selection parameters. */
+
+ field->offset = (hsize_t *)malloc(rank * sizeof(hsize_t));
+ field->count = (hsize_t *)malloc(rank * sizeof(hsize_t));
+
+
+ /* Allocate enough memory for a single cap-slice buffer. */
+
+ field->n = 1;
+ for(d = 1; d < rank; d++)
+ field->n *= field->dims[d];
+
+ field->data = (float *)malloc(field->n * sizeof(float));
+
+
+ /* Release resources. */
+
+ status = H5Sclose(dataspace);
+ status = H5Dclose(dataset);
+
+ return field;
+}
+
+
+herr_t read_field(hid_t file_id, field_t *field, int iii)
+{
+ hid_t dataset;
+ hid_t filespace;
+ hid_t memspace;
+ herr_t status;
+
+ int d;
+
+ if (file_id < 0 || field == NULL)
+ return -1;
+
+ dataset = H5Dopen(file_id, field->name);
+
+ if (dataset < 0)
+ return -1;
+
+ field->offset[0] = iii;
+ field->count[0] = 1;
+ for(d = 1; d < field->rank; d++)
+ {
+ field->offset[d] = 0;
+ field->count[d] = field->dims[d];
+ }
+
+
+ /* DEBUG */
+ printf("Reading cap %d on field %s with offset (", iii, field->name);
+ for(d = 0; d < field->rank; d++) printf("%d,", (int)(field->offset[d]));
+ printf(") and count (");
+ for(d = 0; d < field->rank; d++) printf("%d,", (int)(field->count[d]));
+ printf(")\n");
+ // */
+
+
+ filespace = H5Dget_space(dataset);
+
+ status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET,
+ field->offset, NULL, field->count, NULL);
+
+ memspace = H5Screate_simple(field->rank, field->count, NULL);
+
+ status = H5Dread(dataset, H5T_NATIVE_FLOAT, memspace,
+ filespace, H5P_DEFAULT, field->data);
+
+ status = H5Sclose(filespace);
+ status = H5Sclose(memspace);
+ status = H5Dclose(dataset);
+
+ return 0;
+}
+
+
+herr_t close_field(field_t *field)
+{
+ if (field != NULL)
+ {
+ free(field->dims);
+ free(field->maxdims);
+ free(field->offset);
+ free(field->count);
+ free(field->data);
+ free(field);
+ }
+ return 0;
+}
+
+herr_t get_attribute_str(hid_t obj_id,
+ const char *attr_name,
+ char **data)
+{
+ hid_t attr_id;
+ hid_t attr_type;
+ size_t type_size;
+ herr_t status;
+
+ *data = NULL;
+
+ attr_id = H5Aopen_name(obj_id, attr_name);
+ if (attr_id < 0)
+ return -1;
+
+ attr_type = H5Aget_type(attr_id);
+ if (attr_type < 0)
+ goto out;
+
+ /* Get the size */
+ type_size = H5Tget_size(attr_type);
+ if (type_size < 0)
+ goto out;
+
+ /* malloc enough space for the string, plus 1 for trailing '\0' */
+ *data = (char *)malloc(type_size + 1);
+
+ status = H5Aread(attr_id, attr_type, *data);
+ if (status < 0)
+ goto out;
+
+ /* Set the last character to '\0' in case we are dealing with
+ * null padded or space padded strings
+ */
+ (*data)[type_size] = '\0';
+
+ status = H5Tclose(attr_type);
+ if (status < 0)
+ goto out;
+
+ status = H5Aclose(attr_id);
+ if (status < 0)
+ return -1;
+
+ return 0;
+
+out:
+ H5Tclose(attr_type);
+ H5Aclose(attr_id);
+ if (*data)
+ free(*data);
+ return -1;
+}
+
+herr_t get_attribute_int(hid_t input, const char *name, int *val)
+{
+ hid_t attr_id;
+ hid_t type_id;
+ H5T_class_t type_class;
+ size_t type_size;
+
+ herr_t status;
+
+ char *strval;
+
+ attr_id = H5Aopen_name(input, name);
+ type_id = H5Aget_type(attr_id);
+ type_class = H5Tget_class(type_id);
+ type_size = H5Tget_size(type_id);
+
+ H5Tclose(type_id);
+ H5Aclose(attr_id);
+
+ switch(type_class)
+ {
+ case H5T_STRING:
+ status = get_attribute_str(input, name, &strval);
+ if (status < 0) return -1;
+ *val = atoi(strval);
+ free(strval);
+ return 0;
+ case H5T_INTEGER:
+ status = get_attribute(input, name, H5T_NATIVE_INT, val);
+ if (status < 0) return -1;
+ return 0;
+ default:
+ return -1;
+ }
+
+ return -1;
+}
+
+
+herr_t get_attribute_float(hid_t input, const char *name, float *val)
+{
+ hid_t attr_id;
+ hid_t type_id;
+ H5T_class_t type_class;
+ size_t type_size;
+
+ herr_t status;
+
+ char *strval;
+
+ attr_id = H5Aopen_name(input, name);
+ type_id = H5Aget_type(attr_id);
+ type_class = H5Tget_class(type_id);
+ type_size = H5Tget_size(type_id);
+
+ H5Tclose(type_id);
+ H5Aclose(attr_id);
+
+ switch(type_class)
+ {
+ case H5T_STRING:
+ status = get_attribute_str(input, name, &strval);
+ if (status < 0) return -1;
+ *val = atof(strval);
+ free(strval);
+ return 0;
+ case H5T_FLOAT:
+ status = get_attribute(input, name, H5T_NATIVE_FLOAT, val);
+ if (status < 0) return -1;
+ return 0;
+ default:
+ return -1;
+ }
+
+ return -1;
+}
+
+
+static herr_t get_attribute(hid_t obj_id,
+ const char *attr_name,
+ hid_t mem_type_id,
+ void *data)
+{
+ herr_t status;
+
+ status = get_attribute_mem(obj_id, attr_name, mem_type_id, data);
+ if (status < 0)
+ return -1;
+
+ return 0;
+}
+
+
+static herr_t get_attribute_mem(hid_t obj_id,
+ const char *attr_name,
+ hid_t mem_type_id,
+ void *data)
+{
+ hid_t attr_id;
+ herr_t status;
+
+ attr_id = H5Aopen_name(obj_id, attr_name);
+ if (attr_id < 0)
+ return -1;
+
+ status = H5Aread(attr_id, mem_type_id, data);
+ if (status < 0)
+ {
+ H5Aclose(attr_id);
+ return -1;
+ }
+
+ status = H5Aclose(attr_id);
+ if (status < 0)
+ return -1;
+
+ return 0;
+}
+
+
Added: mc/3D/CitcomS/trunk/visual/h5util.h
===================================================================
--- mc/3D/CitcomS/trunk/visual/h5util.h 2006-12-02 04:15:26 UTC (rev 5421)
+++ mc/3D/CitcomS/trunk/visual/h5util.h 2006-12-02 04:43:50 UTC (rev 5422)
@@ -0,0 +1,48 @@
+/*
+ * h5util.h by Luis Armendariz and Eh Tan.
+ * Copyright (C) 2006, California Institute of Technology.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+
+#include "hdf5.h"
+
+
+typedef struct field_t
+{
+ const char *name;
+
+ int rank;
+ hsize_t *dims;
+ hsize_t *maxdims;
+
+ hsize_t *offset;
+ hsize_t *count;
+
+ int n;
+ float *data;
+
+} field_t;
+
+
+field_t *open_field(hid_t cap, const char *name);
+herr_t read_field(hid_t cap, field_t *field, int iii);
+herr_t close_field(field_t *field);
+
+herr_t get_attribute_str(hid_t obj_id, const char *attr_name, char **data);
+herr_t get_attribute_int(hid_t input, const char *name, int *val);
+herr_t get_attribute_float(hid_t input, const char *name, float *val);
+
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