diff --git a/logger/logger_dump.c b/logger/logger_dump.c
index 2c21bd42c1d147209fb614286d4d07c7bcd5b8a8..8f82706b01677551f6cb3532e668bd4f0faa37bb 100644
--- a/logger/logger_dump.c
+++ b/logger/logger_dump.c
@@ -35,6 +35,9 @@ void logger_dump_init(
/* Set the pointer to the reader. */
dump->reader = reader;
+ /* Set pointers to zero */
+ time_array_init_to_zero(&dump->times);
+
/* Open file, map it and get its size. */
if (reader->verbose > 1)
message("Mapping the dump file.");
@@ -51,14 +54,14 @@ void logger_dump_init(
}
/* Check if the offset are corrupted */
- if (header_are_offset_corrupted(&dump->header)) {
+ if (header_is_corrupted(&dump->header)) {
error("The offsets have been corrupted");
}
/* Reverse offset direction */
if (reader->verbose > 1)
message("Checking if offsets need to be reversed.");
- if (header_are_offset_backward(&dump->header)) {
+ if (header_is_backward(&dump->header)) {
logger_dump_reverse_offset(dump);
}
@@ -94,7 +97,7 @@ void logger_dump_reverse_offset(struct logger_dump *dump) {
struct header *header = &dump->header;
const struct logger_reader *reader = dump->reader;
- if (!header_are_offset_backward(header)) {
+ if (!header_is_backward(header)) {
error("The offset are already reversed.");
}
@@ -102,31 +105,32 @@ void logger_dump_reverse_offset(struct logger_dump *dump) {
#ifdef SWIFT_DEBUG_CHECKS
/* check offset */
if (reader->verbose > 0) {
- message("Check offsets...\n");
- }
- size_t offset_debug = header->offset_first;
- while (offset_debug < dump->dump.file_size) {
- tools_check_offset(header, dump->dump.map, &offset_debug);
+ message("Check offsets...");
}
+
+ for(size_t offset_debug = header->offset_first;
+ offset_debug < dump->dump.file_size;
+ offset_debug = tools_check_offset(reader, offset_debug)) {}
+
if (reader->verbose > 0) {
- message("Check done\n");
+ message("Check done");
}
#endif
/* reverse header offset */
header_change_offset_direction(header, logger_offset_corrupted);
- size_t offset = header->offset_first;
-
/* reverse chunks */
if (reader->verbose > 0) {
- message("Reversing offsets...\n");
- }
- while (offset < dump->dump.file_size) {
- tools_reverse_offset(header, dump->dump.map, &offset);
+ message("Reversing offsets...");
}
+
+ for(size_t offset = header->offset_first;
+ offset < dump->dump.file_size;
+ offset = tools_reverse_offset(header, dump->dump.map, offset)) {}
+
if (reader->verbose > 0) {
- message("Reversing done\n");
+ message("Reversing done");
}
/* reverse header offset */
@@ -135,14 +139,15 @@ void logger_dump_reverse_offset(struct logger_dump *dump) {
#ifdef SWIFT_DEBUG_CHECKS
/* check offset */
if (reader->verbose > 0) {
- message("Check offsets...\n");
- }
- offset_debug = header->offset_first;
- while (offset_debug < dump->dump.file_size) {
- tools_check_offset(header, dump->dump.map, &offset_debug);
+ message("Check offsets...");
}
+
+ for(size_t offset_debug = header->offset_first;
+ offset_debug < dump->dump.file_size;
+ offset_debug = tools_check_offset(reader, offset_debug)) {}
+
if (reader->verbose > 0) {
- message("Check done\n");
+ message("Check done");
}
#endif
diff --git a/logger/logger_header.c b/logger/logger_header.c
index 1a93076f5edc2605b6413fec9e0ab094c9d3f2d9..884b3bcdc0b6cae925631dc2d6c5729789cab08c 100644
--- a/logger/logger_header.c
+++ b/logger/logger_header.c
@@ -90,7 +90,7 @@ void header_change_offset_direction(struct header *h, int new_value) {
h->offset_direction = new_value;
size_t offset = LOGGER_VERSION_SIZE;
- io_write_data(h->dump->dump.map, LOGGER_NUMBER_SIZE, &new_value, &offset);
+ io_write_data(h->dump->dump.map, LOGGER_NUMBER_SIZE, &new_value, offset);
}
/**
@@ -107,23 +107,23 @@ void header_read(struct header *h, struct logger_dump *dump) {
h->dump = dump;
/* read version */
- io_read_data(map, LOGGER_VERSION_SIZE, &h->version, &offset);
+ offset = io_read_data(map, LOGGER_VERSION_SIZE, &h->version, offset);
/* read offset direction */
h->offset_direction = -1;
- io_read_data(map, LOGGER_NUMBER_SIZE, &h->offset_direction, &offset);
+ offset = io_read_data(map, LOGGER_NUMBER_SIZE, &h->offset_direction, offset);
- if (!header_are_offset_forward(h) && !header_are_offset_backward(h) &&
- !header_are_offset_corrupted(h))
+ if (!header_is_forward(h) && !header_is_backward(h) &&
+ !header_is_corrupted(h))
error("Wrong offset value in the header (%i)", h->offset_direction);
/* read offset to first data */
h->offset_first = 0;
- io_read_data(map, LOGGER_OFFSET_SIZE, &h->offset_first, &offset);
+ offset = io_read_data(map, LOGGER_OFFSET_SIZE, &h->offset_first, offset);
/* read name size */
h->name_length = 0;
- io_read_data(map, LOGGER_NUMBER_SIZE, &h->name_length, &offset);
+ offset = io_read_data(map, LOGGER_NUMBER_SIZE, &h->name_length, offset);
/* check if value defined in this file is large enough */
if (STRING_SIZE < h->name_length) {
@@ -132,7 +132,7 @@ void header_read(struct header *h, struct logger_dump *dump) {
/* read number of masks */
h->number_mask = 0;
- io_read_data(map, LOGGER_NUMBER_SIZE, &h->number_mask, &offset);
+ offset = io_read_data(map, LOGGER_NUMBER_SIZE, &h->number_mask, offset);
/* allocate memory */
h->masks = malloc(sizeof(struct mask_data) * h->number_mask);
@@ -140,14 +140,14 @@ void header_read(struct header *h, struct logger_dump *dump) {
/* loop over all masks */
for (size_t i = 0; i < h->number_mask; i++) {
/* read mask name */
- io_read_data(map, h->name_length, h->masks[i].name, &offset);
+ offset = io_read_data(map, h->name_length, h->masks[i].name, offset);
/* get mask value */
h->masks[i].mask = 1 << i;
/* read mask data size */
h->masks[i].size = 0;
- io_read_data(map, LOGGER_NUMBER_SIZE, &h->masks[i].size, &offset);
+ offset = io_read_data(map, LOGGER_NUMBER_SIZE, &h->masks[i].size, offset);
}
if (offset != h->offset_first) {
diff --git a/logger/logger_header.h b/logger/logger_header.h
index 6e18c82e3654e9adc47ec8b7bc8532e5b342a022..a6891126abaae73e4ec25032f969a0c266190023 100644
--- a/logger/logger_header.h
+++ b/logger/logger_header.h
@@ -91,7 +91,7 @@ void header_change_offset_direction(struct header *h, int new_value);
* @brief Check if the offset are forward.
* @param h The #header.
*/
-__attribute__((always_inline)) INLINE static int header_are_offset_forward(
+__attribute__((always_inline)) INLINE static int header_is_forward(
const struct header *h) {
return h->offset_direction == logger_offset_forward;
}
@@ -100,7 +100,7 @@ __attribute__((always_inline)) INLINE static int header_are_offset_forward(
* @brief Check if the offset are backward.
* @param h The #header.
*/
-__attribute__((always_inline)) INLINE static int header_are_offset_backward(
+__attribute__((always_inline)) INLINE static int header_is_backward(
const struct header *h) {
return h->offset_direction == logger_offset_backward;
}
@@ -109,7 +109,7 @@ __attribute__((always_inline)) INLINE static int header_are_offset_backward(
* @brief Check if the offset are corrupted.
* @param h The #header.
*/
-__attribute__((always_inline)) INLINE static int header_are_offset_corrupted(
+__attribute__((always_inline)) INLINE static int header_is_corrupted(
const struct header *h) {
return h->offset_direction == logger_offset_corrupted;
}
diff --git a/logger/logger_io.h b/logger/logger_io.h
index 7fafab84fe34c8aa54464e4f51007939109a208c..b0b94080974d49baec6ca046d472d35e0b12d15a 100644
--- a/logger/logger_io.h
+++ b/logger/logger_io.h
@@ -37,57 +37,64 @@ void io_munmap_file(void *map, size_t file_size);
*
* @param h #header file structure
* @param data Pointer to the data to read.
- * @param offset In: position in the file, Out: shifted by the mask + offset
+ * @param offset position in the file, Out: shifted by the mask + offset
* size
* @param mask mask read
* @param diff_offset offset difference to previous/next corresponding chunk
*
+ * @return offset after the record header
*/
-__attribute__((always_inline)) INLINE static void io_read_mask(
- const struct header *h, void *data, size_t *offset, size_t *mask,
+__attribute__((always_inline)) INLINE static size_t io_read_mask(
+ const struct header *h, void *data, size_t offset, size_t *mask,
size_t *diff_offset) {
/* read mask */
if (mask) {
*mask = 0;
- memcpy(mask, data + *offset, LOGGER_MASK_SIZE);
+ memcpy(mask, data + offset, LOGGER_MASK_SIZE);
}
- *offset += LOGGER_MASK_SIZE;
+ offset += LOGGER_MASK_SIZE;
/* read offset */
if (diff_offset) {
*diff_offset = 0;
- memcpy(diff_offset, data + *offset, LOGGER_OFFSET_SIZE);
+ memcpy(diff_offset, data + offset, LOGGER_OFFSET_SIZE);
}
- *offset += LOGGER_OFFSET_SIZE;
+ offset += LOGGER_OFFSET_SIZE;
+
+ return offset;
}
/**
- * @brief read a single value in a file
+ * @brief read a single value in a file.
*
* @param data Pointer to the data to read.
- * @param size size of the chunk to read
- * @param p pointer where to store the data
- * @param offset In: position to read, Out: shifted by size
+ * @param size size of the chunk to read.
+ * @param p pointer where to store the data.
+ * @param offset position to read.
+
+ * @return offset after the record.
*/
-__attribute__((always_inline)) INLINE static void io_read_data(
- void *data, const size_t size, void *p, size_t *offset) {
- memcpy(p, data + *offset, size);
- *offset += size;
+__attribute__((always_inline)) INLINE static size_t io_read_data(
+ void *data, const size_t size, void *p, size_t offset) {
+ memcpy(p, data + offset, size);
+ return offset + size;
};
/**
- * @brief write a single value in a file
+ * @brief write a single value in a file.
*
* @param data Pointer to the data to read.
- * @param size size of the chunk to write
- * @param p pointer to the data
- * @param offset In: position to write, Out: shifted by size
+ * @param size size of the chunk to write.
+ * @param p pointer to the data.
+ * @param offset position to write.
*
+ * @return offset after the data written.
*/
-__attribute__((always_inline)) INLINE static void io_write_data(
- void *data, const size_t size, const void *p, size_t *offset) {
- memcpy(data + *offset, p, size);
- *offset += size;
+__attribute__((always_inline)) INLINE static size_t io_write_data(
+ void *data, const size_t size, const void *p, size_t offset) {
+ memcpy(data + offset, p, size);
+
+ return offset + size;
};
#endif // __LOGGER_LOGGER_IO_H__
diff --git a/logger/logger_particle.c b/logger/logger_particle.c
index fa2ed36e9a201d52a0c2eac80d5dcbea2e9c139f..8c0227ee3eac4368219a0fc0da762fd85ab2b643 100644
--- a/logger/logger_particle.c
+++ b/logger/logger_particle.c
@@ -19,6 +19,7 @@
#include "logger_particle.h"
#include "logger_header.h"
#include "logger_io.h"
+#include "logger_reader.h"
#include "logger_time.h"
#include "logger_tools.h"
@@ -63,19 +64,19 @@ void logger_particle_init(struct logger_particle *part) {
}
/**
- * @brief Read a single field for a particle
+ * @brief Read a single field for a particle.
*
- * @param part The #logger_particle to update
+ * @param part The #logger_particle to update.
* @param data Pointer to the data to read.
- * @param offset In: read position, Out: input shifted by the required amount of
- * data
- * @param field field to read
- * @param size number of bits to read
+ * @param offset position to read.
+ * @param field field to read.
+ * @param size number of bits to read.
*
+ * @return position after the data read.
*/
-void logger_particle_read_field(struct logger_particle *part, void *map,
- size_t *offset, const char *field,
- const size_t size) {
+size_t logger_particle_read_field(struct logger_particle *part, void *map,
+ size_t offset, const char *field,
+ const size_t size) {
void *p = NULL;
if (strcmp("positions", field) == 0) {
@@ -96,7 +97,7 @@ void logger_particle_read_field(struct logger_particle *part, void *map,
error("Type %s not defined", field);
}
- io_read_data(map, size, p, offset);
+ offset = io_read_data(map, size, p, offset);
if (strcmp("consts", field) == 0) {
part->mass = 0;
@@ -107,67 +108,81 @@ void logger_particle_read_field(struct logger_particle *part, void *map,
p -= sizeof(float);
free(p);
}
+
+ return offset;
}
/**
* @brief Read a particle in the dump file.
*
+ * @param reader The #logger_reader.
* @param part The #logger_particle to update.
- * @param h #header structure of the file
- * @param map file mapping
- * @param offset offset of the chunk to read (update it to the end of the chunk)
+ * @param offset offset of the chunk to read.
* @param time time to interpolate (if #logger_reader_type is an interpolating
- * one)
- * @param reader #logger_reader_type
- * @param times #time_array times in the dump
+ * one).
+ * @param reader_type #logger_reader_type.
*
+ * @return position after the record.
*/
-void logger_particle_read(struct logger_particle *part, const struct header *h,
- void *map, size_t *offset, const double time,
- const int reader, struct time_array *times) {
+size_t logger_particle_read(struct logger_particle *part, const struct logger_reader *reader,
+ size_t offset, const double time,
+ const enum logger_reader_type reader_type) {
+
+ const struct header *h = &reader->dump.header;
+ void *map = reader->dump.dump.map;
+
+ const struct time_array *times = &reader->dump.times;
+
size_t mask = 0;
size_t h_offset = 0;
logger_particle_init(part);
- io_read_mask(h, map, offset, &mask, &h_offset);
+ offset = io_read_mask(h, map, offset, &mask, &h_offset);
if (mask != 127) error("Unexpected mask: %lu", mask);
for (size_t i = 0; i < h->number_mask; i++) {
if (mask & h->masks[i].mask) {
- logger_particle_read_field(part, map, offset, h->masks[i].name,
- h->masks[i].size);
+ offset = logger_particle_read_field(part, map, offset, h->masks[i].name,
+ h->masks[i].size);
}
}
- if (times) /* move offset by 1 in order to be in the required chunk */
- part->time = time_array_get_time(times, *offset - 1);
+ if (times) {
+ /* move offset by 1 in order to be in the required chunk */
+ part->time = time_array_get_time(times, offset - 1);
+ }
else
part->time = -1;
/* end of const case */
- if (reader == logger_reader_const) return;
+ if (reader_type == logger_reader_const)
+ return offset;
/* read next particle */
struct logger_particle part_next;
- if (!header_are_offset_forward(h)) {
+ if (!header_is_forward(h)) {
error("Cannot read a particle with non forward offsets.");
}
- if (h_offset == 0) return;
+ if (h_offset == 0)
+ return offset;
+
/* get absolute offset of next particle */
- h_offset += *offset - header_get_mask_size(h, mask) - LOGGER_MASK_SIZE -
+ h_offset += offset - header_get_mask_size(h, mask) - LOGGER_MASK_SIZE -
LOGGER_OFFSET_SIZE;
part_next.time = time_array_get_time(times, h_offset);
/* previous part exists */
- logger_particle_read(&part_next, h, map, &h_offset, part_next.time,
- logger_reader_const, times);
+ h_offset = logger_particle_read(&part_next, reader, h_offset, part_next.time,
+ logger_reader_const);
logger_particle_interpolate(part, &part_next, time);
+
+ return offset;
}
/**
diff --git a/logger/logger_particle.h b/logger/logger_particle.h
index 112ad28962c31ebad98fac8b874475c83c0b3a08..3493f13dc1d83d63f74ad99f2fd513d6f9f7198b 100644
--- a/logger/logger_particle.h
+++ b/logger/logger_particle.h
@@ -28,6 +28,8 @@
#define DIM 3
+struct logger_reader;
+
/**
* @brief Store the data from a chunk.
*
@@ -83,14 +85,14 @@ enum logger_reader_type {
void logger_particle_print(const struct logger_particle *p);
-void logger_particle_read(struct logger_particle *part, const struct header *h,
- void *map, size_t *offset, const double time,
- const int reader, struct time_array *times);
+size_t logger_particle_read(struct logger_particle *part, const struct logger_reader *reader,
+ size_t offset, const double time,
+ const enum logger_reader_type reader_type);
void logger_particle_init(struct logger_particle *part);
-void logger_particle_read_field(struct logger_particle *part, void *map,
- size_t *offset, const char *field,
+size_t logger_particle_read_field(struct logger_particle *part, void *map,
+ size_t offset, const char *field,
const size_t size);
void logger_particle_interpolate(struct logger_particle *part_curr,
diff --git a/logger/logger_python_wrapper.c b/logger/logger_python_wrapper.c
index 4c8c2d0b04a00f1f3a9f15af397ecd3fb84c159b..4fe72bf10888fd0a879ec9ce0fc0b2d9bf03553c 100644
--- a/logger/logger_python_wrapper.c
+++ b/logger/logger_python_wrapper.c
@@ -56,7 +56,7 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
PyArrayObject *id = NULL;
size_t time_offset;
- int verbose = 0;
+ int verbose = 2;
/* parse arguments */
@@ -123,14 +123,14 @@ static PyObject *loadFromIndex(__attribute__((unused)) PyObject *self,
if (verbose > 1)
message("Reading particles.");
+
/* loop over all particles */
for (npy_intp i = 0; i < PyArray_DIMS(offset)[0]; i++) {
struct logger_particle part;
- size_t *offset_particle = (size_t *)PyArray_GETPTR1(offset, i);
+ size_t offset_particle = *(size_t *)PyArray_GETPTR1(offset, i);
- logger_particle_read(&part, &reader.dump.header, reader.dump.dump.map, offset_particle, time,
- logger_reader_lin, &reader.dump.times);
+ logger_particle_read(&part, &reader, offset_particle, time, logger_reader_lin);
double *dtmp;
float *ftmp;
diff --git a/logger/logger_time.c b/logger/logger_time.c
index 71247341c0e9cdd1b2838be08ebaf1287073b61f..758cbbd0699f59434d48c945066f815454192ebe 100644
--- a/logger/logger_time.c
+++ b/logger/logger_time.c
@@ -26,19 +26,24 @@
*
* @param timestamp timestamp read
* @param time time read
- * @param h #header file structure
- * @param map file mapping
- * @param offset In: position in the file, Out: shifted by the timestamp
+ * @param reader The #logger_reader
+ * @param offset position in the file
+ *
+ * @return position after the timestamp
*/
-void time_read(integertime_t *timestamp, double *time, const struct header *h,
- void *map, size_t *offset) {
+size_t time_read(integertime_t *timestamp, double *time, const struct logger_reader *reader,
+ size_t offset) {
+
+ const struct header *h = &reader->dump.header;
+ void *map = h->dump->dump.map;
+
size_t mask = 0;
size_t prev_offset = 0;
*timestamp = 0;
*time = 0;
/* read chunck header */
- io_read_mask(h, map, offset, &mask, &prev_offset);
+ offset = io_read_mask(h, map, offset, &mask, &prev_offset);
#ifdef SWIFT_DEBUG_CHECKS
@@ -51,33 +56,44 @@ void time_read(integertime_t *timestamp, double *time, const struct header *h,
#endif
/* read data */
- // TODO
- io_read_data(map, sizeof(unsigned long long int), timestamp, offset);
- io_read_data(map, sizeof(double), time, offset);
+ offset = io_read_data(map, sizeof(unsigned long long int), timestamp, offset);
+ offset = io_read_data(map, sizeof(double), time, offset);
+
+ return offset;
}
/**
* @brief get offset of first timestamp
*
* @param h file #header
- * @param map file mapping
- * @param offset out: offset of first timestamp
+ * @return offset of first timestamp
*
*/
-void time_first_timestamp(const struct header *h, void *map, size_t *offset) {
- *offset = h->offset_first;
+size_t time_first_timestamp(const struct header *h) {
+ size_t offset = h->offset_first;
+ void *map = h->dump->dump.map;
int i = header_get_field_index(h, "timestamp");
if (i == -1) error("Time stamp not present in header");
- size_t tmp = *offset;
size_t mask = 0;
io_read_mask(h, map, offset, &mask, NULL);
if (mask != h->masks[i].mask) error("Dump should begin by timestep");
- *offset = tmp;
+ return h->offset_first;
+}
+
+/**
+ * @brief Initialize an empty time array.
+ *
+ * @param t #time_array to initialize.
+ * @param dump The #logger_dump.
+ */
+void time_array_init_to_zero(struct time_array *t) {
+ t->next = NULL;
+ t->prev = NULL;
}
/**
@@ -91,21 +107,19 @@ void time_array_init(struct time_array *t, struct logger_dump *dump) {
t->next = NULL;
t->prev = NULL;
- /* get first time stamp */
- size_t offset = 0;
- time_first_timestamp(&dump->header, dump->dump.map, &offset);
-
integertime_t timestamp = 0;
double time = 0;
/* get file size */
size_t file_size = dump->dump.file_size;
+ /* get first time stamp */
+ size_t offset = time_first_timestamp(&dump->header);
while (offset < file_size) {
/* read time */
t->offset = offset;
size_t tmp_offset = offset;
- time_read(×tamp, &time, &dump->header, dump->dump.map, &tmp_offset);
+ tmp_offset = time_read(×tamp, &time, dump->reader, tmp_offset);
t->timestamp = timestamp;
t->time = time;
@@ -150,7 +164,7 @@ integertime_t time_array_get_integertime(struct time_array *t,
*
* @return time of the chunk
*/
-double time_array_get_time(struct time_array *t, const size_t offset) {
+double time_array_get_time(const struct time_array *t, const size_t offset) {
const struct time_array *tmp = time_array_get_time_array(t, offset);
return tmp->time;
}
@@ -163,22 +177,19 @@ double time_array_get_time(struct time_array *t, const size_t offset) {
*
* @return pointer to the requested #time_array
*/
-struct time_array *time_array_get_time_array(struct time_array *t,
+struct time_array *time_array_get_time_array(const struct time_array *t,
const size_t offset) {
#ifdef SWIFT_DEBUG_CHECKS
- if (!t) return 0;
+ if (!t) error("NULL pointer");
#endif
- while (t->next) {
- if (t->offset > offset) break;
+ const struct time_array *tmp;
+ for(tmp = t; tmp->next && tmp->offset <= offset; tmp = tmp->next)
+ {}
- t = t->next;
- }
+ if (tmp->prev == NULL) return (struct time_array *) tmp;
- if (t->prev == NULL) return t;
-
- struct time_array *tmp = t->prev;
- return tmp;
+ return (struct time_array *) tmp->prev;
}
/**
@@ -188,10 +199,9 @@ struct time_array *time_array_get_time_array(struct time_array *t,
*/
void time_array_free(struct time_array *t) {
struct time_array *tmp;
- while (t->next) {
+ for(tmp = t; t->next; t = tmp) {
tmp = t->next;
free(t);
- t = tmp;
}
}
@@ -204,13 +214,15 @@ void time_array_print(const struct time_array *t) {
size_t threshold = 4;
size_t n = time_array_count(t);
- size_t i = 0;
size_t up_threshold = n - threshold;
printf("Times (size %lu): [%lli (%g)", n, t->timestamp, t->time);
- while (t->next) {
- i += 1;
+ for(size_t i = 1; i < n; i++) {
+ /* The last time_array does not have a next */
+ if (!t->next)
+ error("Next pointer not initialized %li", i);
+
t = t->next;
if (i < threshold || i > up_threshold)
printf(", %lli (%g)", t->timestamp, t->time);
@@ -230,13 +242,12 @@ void time_array_print_offset(const struct time_array *t) {
size_t threshold = 4;
size_t n = time_array_count(t);
- size_t i = 0;
size_t up_threshold = n - threshold;
printf("Times (size %lu): [%lu", n, t->offset);
- while (t->next) {
- i += 1;
+
+ for(size_t i = 1; i < n; i++) {
t = t->next;
if (i < threshold || i > up_threshold) printf(", %lu", t->offset);
@@ -255,8 +266,7 @@ void time_array_print_offset(const struct time_array *t) {
*/
size_t time_array_count(const struct time_array *t) {
size_t count = 1;
- while (t->next) {
- t = t->next;
+ for(; t->next; t = t->next) {
count += 1;
}
diff --git a/logger/logger_time.h b/logger/logger_time.h
index 004c3b4e3e9e83a1bfa8cf840951dc0e97686349..b2f56ef3ccd95f2b33ed181dbb25f410d169852a 100644
--- a/logger/logger_time.h
+++ b/logger/logger_time.h
@@ -25,6 +25,8 @@
typedef char timebin_t;
typedef long long integertime_t;
+struct logger_reader;
+
/**
* @brief This structure contains all the timestamp.
*
@@ -59,18 +61,26 @@ struct time_array {
size_t offset;
};
-void time_read(integertime_t *timestamp, double *time, const struct header *h,
- void *map, size_t *offset);
+size_t time_read(integertime_t *timestamp, double *time,
+ const struct logger_reader *reader, size_t offset);
+
+void time_array_init_to_zero(struct time_array *t);
void time_array_init(struct time_array *t, struct logger_dump *dump);
-integertime_t time_array_get_integertime(struct time_array *t,
- const size_t offset);
-double time_array_get_time(struct time_array *t, const size_t offset);
-struct time_array *time_array_get_time_array(struct time_array *t,
- const size_t offset);
+
+integertime_t time_array_get_integertime(struct time_array *t, const size_t offset);
+
+double time_array_get_time(const struct time_array *t, const size_t offset);
+
+struct time_array *time_array_get_time_array(const struct time_array *t, const size_t offset);
+
void time_array_free(struct time_array *t);
+
void time_array_print(const struct time_array *t);
+
void time_array_print_offset(const struct time_array *t);
+
size_t time_array_count(const struct time_array *t);
-void time_first_timestamp(const struct header *h, void *map, size_t *offset);
+
+size_t time_first_timestamp(const struct header *h);
#endif // __LOGGER_LOGGER_TIMELINE_H__
diff --git a/logger/logger_tools.c b/logger/logger_tools.c
index 112a000d64fac5b8ff86f9a470dc4fc006f4b5c4..24a654920d511bbe47b91a40c5ad9c7c182b9899 100644
--- a/logger/logger_tools.c
+++ b/logger/logger_tools.c
@@ -19,6 +19,7 @@
#include "logger_tools.h"
#include "logger_header.h"
#include "logger_io.h"
+#include "logger_reader.h"
#include "logger_particle.h"
@@ -36,9 +37,9 @@
*/
int tools_get_next_chunk(const struct header *h, void *map, size_t *offset,
size_t file_size) {
- if (header_are_offset_forward(h))
+ if (header_is_forward(h))
return _tools_get_next_chunk_forward(h, map, offset);
- if (header_are_offset_backward(h))
+ if (header_is_backward(h))
return _tools_get_next_chunk_backward(h, map, offset, file_size);
else
error("Offsets are corrupted");
@@ -58,7 +59,7 @@ int _tools_get_next_chunk_forward(const struct header *h, void *map,
size_t diff_offset = 0;
/* read offset */
- io_read_mask(h, map, offset, NULL, &diff_offset);
+ *offset = io_read_mask(h, map, *offset, NULL, &diff_offset);
if (diff_offset == 0) return -1;
@@ -89,7 +90,7 @@ int _tools_get_next_chunk_backward(const struct header *h, void *map,
while (current_offset < file_size) {
size_t mask = 0;
size_t prev_offset;
- io_read_mask(h, map, ¤t_offset, &mask, &prev_offset);
+ current_offset = io_read_mask(h, map, current_offset, &mask, &prev_offset);
prev_offset = current_offset - prev_offset - chunk_header;
if (*offset == prev_offset) {
@@ -104,32 +105,34 @@ int _tools_get_next_chunk_backward(const struct header *h, void *map,
}
/**
- * @brief switch side offset
+ * @brief switch side offset.
*
* From current chunk, switch side of the offset of the previous one.
- * @param h #header structure of the file
- * @param map file mapping
- * @param offset In: initial offset, Out: offset of next chunk
+ * @param h #header structure of the file.
+ * @param map file mapping.
+ * @param position of the record.
*
+ * @return position after the record.
*/
-void tools_reverse_offset(const struct header *h, void *map, size_t *offset) {
+size_t tools_reverse_offset(const struct header *h, void *map, size_t offset) {
size_t mask = 0;
size_t prev_offset = 0;
- const size_t cur_offset = *offset;
+ const size_t cur_offset = offset;
/* read mask + offset */
- io_read_mask(h, map, offset, &mask, &prev_offset);
+ offset = io_read_mask(h, map, offset, &mask, &prev_offset);
/* write offset of zero (in case it is the last chunk) */
const size_t zero = 0;
- *offset -= LOGGER_OFFSET_SIZE;
- io_write_data(map, LOGGER_OFFSET_SIZE, &zero, offset);
+ offset -= LOGGER_OFFSET_SIZE;
+ offset = io_write_data(map, LOGGER_OFFSET_SIZE, &zero, offset);
/* set offset after current chunk */
- *offset += header_get_mask_size(h, mask);
+ offset += header_get_mask_size(h, mask);
/* first chunks do not have a previous partner */
- if (prev_offset == cur_offset) return;
+ if (prev_offset == cur_offset)
+ return offset;
if (prev_offset > cur_offset)
error("Unexpected offset, header %lu, current %lu", prev_offset,
@@ -137,18 +140,20 @@ void tools_reverse_offset(const struct header *h, void *map, size_t *offset) {
/* modify previous offset */
size_t abs_prev_offset = cur_offset - prev_offset + LOGGER_MASK_SIZE;
- io_write_data(map, LOGGER_OFFSET_SIZE, &prev_offset, &abs_prev_offset);
+ abs_prev_offset = io_write_data(map, LOGGER_OFFSET_SIZE, &prev_offset, abs_prev_offset);
#ifdef SWIFT_DEBUG_CHECKS
size_t prev_mask = 0;
abs_prev_offset -= LOGGER_MASK_SIZE + LOGGER_OFFSET_SIZE;
- io_read_mask(h, map, &abs_prev_offset, &prev_mask, NULL);
+ abs_prev_offset = io_read_mask(h, map, abs_prev_offset, &prev_mask, NULL);
if (prev_mask != mask)
- error("Unexpected mask: %lu (at %lu), got %lu (at %lu)", mask, *offset,
+ error("Unexpected mask: %lu (at %lu), got %lu (at %lu)", mask, offset,
prev_mask, prev_offset);
#endif // SWIFT_DEBUG_CHECKS
+
+ return offset;
}
/**
@@ -156,29 +161,32 @@ void tools_reverse_offset(const struct header *h, void *map, size_t *offset) {
*
* Compare the mask with the one pointed by the header.
* if the chunk is a particle, check the id too.
- * @param h #header structure of the file
- * @param map file mapping
- * @param offset In: chunk offset, Out: offset after the chunk
*
- * @return error code
+ * @param reader The #logger_reader.
+ * @param offset position of the record.
+ *
+ * @return position after the record.
*/
-void tools_check_offset(const struct header *h, void *map, size_t *offset) {
+size_t tools_check_offset(const struct logger_reader *reader, size_t offset) {
#ifndef SWIFT_DEBUG_CHECKS
error("Should not check in non debug mode");
#endif
- size_t tmp = *offset;
+ const struct header *h = &reader->dump.header;
+ void *map = reader->dump.dump.map;
+
+ size_t tmp = offset;
size_t mask;
size_t pointed_offset;
/* read mask + offset */
- io_read_mask(h, map, offset, &mask, &pointed_offset);
+ offset = io_read_mask(h, map, offset, &mask, &pointed_offset);
/* get absolute offset */
- if (header_are_offset_forward(h))
+ if (header_is_forward(h))
pointed_offset += tmp;
- if (header_are_offset_backward(h)) {
+ else if (header_is_backward(h)) {
if (tmp < pointed_offset)
error("Offset too large (%lu) at %lu with mask %lu", pointed_offset, tmp,
mask);
@@ -189,31 +197,36 @@ void tools_check_offset(const struct header *h, void *map, size_t *offset) {
}
/* set offset after current chunk */
- *offset += header_get_mask_size(h, mask);
+ offset += header_get_mask_size(h, mask);
- if (pointed_offset == tmp || pointed_offset == 0) return;
+ if (pointed_offset == tmp || pointed_offset == 0)
+ return offset;
/* read mask of the pointed chunk */
size_t pointed_mask = 0;
- io_read_mask(h, map, &pointed_offset, &pointed_mask, NULL);
+ pointed_offset = io_read_mask(h, map, pointed_offset, &pointed_mask, NULL);
/* check masks */
if (pointed_mask != mask)
error("Error in the offset (mask %lu != %lu) at %lu and %lu", mask,
pointed_mask,
- *offset - header_get_mask_size(h, mask) - LOGGER_MASK_SIZE -
- LOGGER_OFFSET_SIZE,
+ offset - header_get_mask_size(h, mask) - LOGGER_MASK_SIZE -
+ LOGGER_OFFSET_SIZE,
pointed_offset - LOGGER_MASK_SIZE - LOGGER_OFFSET_SIZE);
- if (pointed_mask == 128) return;
+ if (pointed_mask == 128)
+ return offset;
struct logger_particle part;
- logger_particle_read(&part, h, map, &tmp, 0, logger_reader_const, NULL);
+ tmp = logger_particle_read(&part, reader, tmp, 0, logger_reader_const);
size_t id = part.id;
tmp = pointed_offset - LOGGER_MASK_SIZE - LOGGER_OFFSET_SIZE;
- logger_particle_read(&part, h, map, &tmp, 0, logger_reader_const, NULL);
+ tmp = logger_particle_read(&part, reader, tmp, 0, logger_reader_const);
if (id != part.id)
error("Offset wrong, id incorrect (%lu != %lu) at %lu", id, part.id, tmp);
+
+ return offset;
}
+
diff --git a/logger/logger_tools.h b/logger/logger_tools.h
index 7bdaeb8f9323224e79f56b096ec665b6266dab08..e2e2eba3ea4a46de16c32467f6850df50f804c3d 100644
--- a/logger/logger_tools.h
+++ b/logger/logger_tools.h
@@ -41,6 +41,7 @@
#define STRING_SIZE 200
struct header;
+struct logger_reader;
#define error(s, ...) \
({ \
@@ -62,7 +63,7 @@ int _tools_get_next_chunk_backward(const struct header *h, void *map,
size_t *offset, size_t file_size);
int _tools_get_next_chunk_forward(const struct header *h, void *map,
size_t *offset);
-void tools_reverse_offset(const struct header *h, void *map, size_t *offset);
-void tools_check_offset(const struct header *h, void *map, size_t *offset);
+size_t tools_reverse_offset(const struct header *h, void *map, size_t offset);
+size_t tools_check_offset(const struct logger_reader *reader, size_t offset);
#endif //__LOGGER_LOGGER_TOOLS_H__
diff --git a/logger/python/reader_example.py b/logger/python/reader_example.py
index d3b40254b0bbd8c1409279d63a671204f7dd635b..aadc8f29402b021536f0f96297cb5fa9fae0c104 100644
--- a/logger/python/reader_example.py
+++ b/logger/python/reader_example.py
@@ -14,7 +14,7 @@ import liblogger as logger
# Get filenames
if len(sys.argv) != 3:
print("WARNING missing arguments. Will use the default ones")
- index = "../../examples/SedovBlast_3D/index_0005.hdf5"
+ index = "../../examples/SedovBlast_3D/index_0002.hdf5"
dump = "../../examples/SedovBlast_3D/index.dump"
else:
index = sys.argv[-1]