Logger: cleanup the code

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
 

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) {

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;
 }

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__

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;
 }
 
 /**

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,

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;

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(&timestamp, &time, &dump->header, dump->dump.map, &tmp_offset);
+    tmp_offset = time_read(&timestamp, &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->