Logger: still cleaning

logger/Makefile.am

@@ -43,11 +43,11 @@ lib_LTLIBRARIES = liblogger.la
 
 # List required headers
 include_HEADERS = logger_header.h logger_io.h logger_particle.h logger_time.h logger_tools.h logger_reader.h \
-	logger_index.h logger_dump.h
+	logger_index.h logger_logfile.h
 
 # Common source files
 AM_SOURCES = logger_header.c logger_io.c logger_particle.c logger_time.c logger_tools.c logger_reader.c \
-	logger_dump.c
+	logger_logfile.c
 if HAVEPYTHON
 AM_SOURCES += logger_python_wrapper.c
 endif

logger/logger_header.c

@@ -18,9 +18,10 @@
  ******************************************************************************/
 #include "logger_header.h"
 
+#include "logger_reader.h"
 #include "logger_io.h"
 #include "logger_tools.h"
-#include "logger_dump.h"
+#include "logger_logfile.h"
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -43,22 +44,22 @@ void header_print(const struct header *h) {
   message("Debug checks enabled");
 #endif
   message("Version:          %s", h->version);
-  message("First Offset:     %lu", h->offset_first);
+  message("First Offset:     %lu", h->offset_first_record);
   message("Offset direction: %s", logger_offset_name[h->offset_direction]);
   message("Number masks:     %lu", h->number_mask);
 
   for (size_t i = 0; i < h->number_mask; i++) {
-    message("\tMask:  %s", h->masks[i].name);
-    message("\tValue: %u", h->masks[i].mask);
-    message("\tSize:  %i", h->masks[i].size);
+    message("  Mask:  %s", h->masks[i].name);
+    message("  Value: %u", h->masks[i].mask);
+    message("  Size:  %i", h->masks[i].size);
     message("");
   }
 };
 
 /**
- * @brief free allocated memory
+ * @brief free allocated memory.
  *
- * @param h The #header
+ * @param h The #header.
  */
 void header_free(struct header *h) { free(h->masks); };
 
@@ -80,34 +81,49 @@ int header_get_field_index(const struct header *h, const char *field) {
 };
 
 /**
- * @brief Inverse the offset direction
+ * @brief Inverse the offset direction.
  *
- * @param h #header file structure
- * @param new_value The new value to write
+ * @param h #header file structure.
+ * @param new_value The new value to write.
  *
  */
-void header_change_offset_direction(struct header *h, int new_value) {
+void header_change_offset_direction(struct header *h, enum logger_offset_direction new_value) {
   h->offset_direction = new_value;
-  size_t offset = LOGGER_VERSION_SIZE;
+  /* Skip file format and version numbers */
+  size_t offset = LOGGER_VERSION_SIZE + 2 * sizeof(int);
 
-  io_write_data(h->dump->dump.map, LOGGER_NUMBER_SIZE, &new_value, offset);
+  io_write_data(h->log->log.map, LOGGER_NUMBER_SIZE, &new_value, offset);
 }
 
 /**
- * @brief read the logger header
+ * @brief read the logger header.
  *
  * @param h out: The #header.
- * @param dump The #logger_dump.
+ * @param log The #logger_logfile.
  */
-void header_read(struct header *h, struct logger_dump *dump) {
+void header_read(struct header *h, struct logger_logfile *log) {
   size_t offset = 0;
-  void *map = dump->dump.map;
+  void *map = log->log.map;
+
+  /* Set pointer to log */
+  h->log = log;
+
+  /* read file format */
+  char file_format[STRING_SIZE];
+  offset = io_read_data(map, LOGGER_VERSION_SIZE, &file_format, offset);
+  if (strcmp(file_format, "SWIFT_LOGGER"))
+    error("Wrong file format");
+
+  /* Read major version */
+  int major;
+  offset = io_read_data(map, sizeof(int), &major, offset);
 
-  /* Set pointer to dump */
-  h->dump = dump;
+  /* Read minor version */
+  int minor;
+  offset = io_read_data(map, sizeof(int), &minor, offset);
 
-  /* read version */
-  offset = io_read_data(map, LOGGER_VERSION_SIZE, &h->version, offset);
+  if (h->log->reader->verbose > 0)
+    message("File version %i.%i", major, minor);
 
   /* read offset direction */
   offset = io_read_data(map, LOGGER_NUMBER_SIZE, &h->offset_direction, offset);
@@ -116,15 +132,15 @@ void header_read(struct header *h, struct logger_dump *dump) {
       !header_is_corrupted(h))
     error("Wrong offset value in the header (%i)", h->offset_direction);
 
-  /* read offset to first data */
-  offset = io_read_data(map, LOGGER_OFFSET_SIZE, &h->offset_first, offset);
+  /* read offset to first record */
+  offset = io_read_data(map, LOGGER_OFFSET_SIZE, &h->offset_first_record, offset);
 
   /* read name size */
   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) {
-    error("Name too large in dump file");
+    error("Name too large in log file");
   }
 
   /* read number of masks */
@@ -145,22 +161,22 @@ void header_read(struct header *h, struct logger_dump *dump) {
     offset = io_read_data(map, LOGGER_NUMBER_SIZE, &h->masks[i].size, offset);
   }
 
-  if (offset != h->offset_first) {
+  if (offset != h->offset_first_record) {
     header_print(h);
-    error("Wrong header size (in header %zi, current %zi)", h->offset_first,
+    error("Wrong header size (in header %zi, current %zi)", h->offset_first_record,
           offset);
   }
 };
 
 /**
- * @brief count number of bits in a given mask
+ * @brief Count number of bits in a given mask (without the record header).
  *
- * @param h #header file structure
- * @param mask mask to compute
+ * @param h #header file structure.
+ * @param mask Mask to compute.
  *
- * @return number of bits in mask
+ * @return number of bits in mask.
  */
-size_t header_get_mask_size(const struct header *h, const size_t mask) {
+size_t header_get_record_size_from_mask(const struct header *h, const size_t mask) {
   size_t count = 0;
   for (size_t i = 0; i < h->number_mask; i++) {
     if (mask & h->masks[i].mask) {

logger/logger_header.h

@@ -43,7 +43,7 @@ enum logger_offset_direction {
 extern const char *logger_offset_name[];
 
 
-struct logger_dump;
+struct logger_logfile;
 
 /**
  * @brief This structure contains everything from the file header.
@@ -60,8 +60,8 @@ struct header {
   /* Logger version. */
   char version[STRING_SIZE];
 
-  /* Offset of the first header. */
-  size_t offset_first;
+  /* Offset of the first record. */
+  size_t offset_first_record;
 
   /* Number of bytes for names. */
   size_t name_length;
@@ -72,19 +72,19 @@ struct header {
   /* List of masks. */
   struct mask_data *masks;
 
-  /* Direction of the offset in the chunks. */
+  /* Direction of the offset in the records. */
   enum logger_offset_direction offset_direction;
 
-  /* The corresponding dump */
-  struct logger_dump *dump;
+  /* The corresponding log */
+  struct logger_logfile *log;
 };
 
 void header_print(const struct header *h);
 void header_free(struct header *h);
 int header_get_field_index(const struct header *h, const char *field);
-void header_read(struct header *h, struct logger_dump *dump);
+void header_read(struct header *h, struct logger_logfile *log);
 size_t header_get_mask_size(const struct header *h, const size_t mask);
-void header_change_offset_direction(struct header *h, int new_value);
+void header_change_offset_direction(struct header *h, enum logger_offset_direction new_value);
 
 
 /**

logger/logger_io.c

@@ -26,11 +26,11 @@
 #include "logger_tools.h"
 
 /**
- * @brief get the size of a file
+ * @brief get the size of a file.
  *
- * @param fd file id
+ * @param fd file id.
  *
- * @return file size
+ * @return file size.
  */
 size_t io_get_file_size(int fd) {
   struct stat s;
@@ -69,9 +69,9 @@ void *io_mmap_file(char *filename, size_t *file_size) {
 }
 
 /**
- * @brief Unmap a file
+ * @brief Unmap a file.
  *
- * @param map file mapping
+ * @param map file mapping.
  * @param file_size The file size.
  *
  */

logger/logger_io.h

@@ -33,16 +33,16 @@ void *io_mmap_file(char *filename, size_t *file_size);
 void io_munmap_file(void *map, size_t file_size);
 
 /**
- * @brief read a mask with its offset
+ * @brief read a mask with its offset.
  *
- * @param h #header file structure
+ * @param h #header file structure.
  * @param data Pointer to the data to read.
- * @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
+ * @param offset position in the file.
+ * @param mask mask read from the data.
+ * @param diff_offset offset difference to previous/next corresponding record read.
+ * from the data.
  *
- * @return offset after the record header
+ * @return offset after the record header.
  */
 __attribute__((always_inline)) INLINE static size_t io_read_mask(
     const struct header *h, void *data, size_t offset, size_t *mask,
@@ -68,11 +68,11 @@ __attribute__((always_inline)) INLINE static size_t io_read_mask(
  * @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 size size of the data to read.
  * @param p pointer where to store the data.
  * @param offset position to read.
 
- * @return offset after the record.
+ * @return offset after the data written.
  */
 __attribute__((always_inline)) INLINE static size_t io_read_data(
     void *data, const size_t size, void *p, size_t offset) {
@@ -84,7 +84,7 @@ __attribute__((always_inline)) INLINE static size_t io_read_data(
  * @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 size size of the data to write.
  * @param p pointer to the data.
  * @param offset position to write.
  *

logger/logger_dump.c → logger/logger_logfile.c

@@ -16,62 +16,62 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  *
  ******************************************************************************/
-#include "logger_dump.h"
+#include "logger_logfile.h"
 #include "logger_reader.h"
 #include "logger_io.h"
 
 /**
- * @brief Initialize the #logger_dump.
+ * @brief Initialize the #logger_logfile.
  *
  * If required this function will also reverse the offsets.
- * @param dump The #logger_dump.
- * @param filename the dump's filename.
+ * @param log The #logger_logfile.
+ * @param filename the log's filename.
  * @param reader The #logger_reader.
  */
-void logger_dump_init(
-    struct logger_dump *dump, char *filename,
+void logger_logfile_init(
+    struct logger_logfile *log, char *filename,
     struct logger_reader *reader) {
 
   /* Set the pointer to the reader. */
-  dump->reader = reader;
+  log->reader = reader;
 
   /* Set pointers to zero */
-  time_array_init_to_zero(&dump->times);
+  time_array_init_to_zero(&log->times);
 
   /* Open file, map it and get its size. */
   if (reader->verbose > 1)
-    message("Mapping the dump file.");
-  dump->dump.map = io_mmap_file(filename, &dump->dump.file_size);
+    message("Mapping the log file.");
+  log->log.map = io_mmap_file(filename, &log->log.file_size);
 
   /* Read header. */
   if (reader->verbose > 1)
     message("Reading the header.");
-  header_read(&dump->header, dump);
+  header_read(&log->header, log);
 
   /* Print the header. */
   if (reader->verbose > 0) {
-    header_print(&dump->header);
+    header_print(&log->header);
   }
 
   /* Check if the offset are corrupted */
-  if (header_is_corrupted(&dump->header)) {
+  if (header_is_corrupted(&log->header)) {
     error("The offsets have been corrupted");
   }
 
   /* Reverse offset direction */
   if (reader->verbose > 1)
     message("Checking if offsets need to be reversed.");
-  if (header_is_backward(&dump->header)) {
-    logger_dump_reverse_offset(dump);
+  if (header_is_backward(&log->header)) {
+    logger_logfile_reverse_offset(log);
   }
 
   /* Initialize the time array */
   if (reader->verbose > 1)
     message("Reading the time stamps.");
-  time_array_init(&dump->times, dump);
+  time_array_init(&log->times, log);
 
   if (reader->verbose > 0) {
-    time_array_print(&dump->times);
+    time_array_print(&log->times);
   }
 
 }
@@ -79,23 +79,23 @@ void logger_dump_init(
 /**
  * @brief Free the allocated memory and unmap the file.
  *
- * @param dump The #logger_dump.
+ * @param log The #logger_logfile.
  */
-void logger_dump_free(struct logger_dump *dump) {
-  io_munmap_file(dump->dump.map, dump->dump.file_size);
+void logger_logfile_free(struct logger_logfile *log) {
+  io_munmap_file(log->log.map, log->log.file_size);
 
 }
 
 
 /**
- * @brief Reverse offset in dump file
+ * @brief Reverse offset in log file
  *
- * @param dump The #logger_dump
+ * @param log The #logger_logfile
  */
-void logger_dump_reverse_offset(struct logger_dump *dump) {
+void logger_logfile_reverse_offset(struct logger_logfile *log) {
 
-  struct header *header = &dump->header;
-  const struct logger_reader *reader = dump->reader;
+  struct header *header = &log->header;
+  const struct logger_reader *reader = log->reader;
 
   if (!header_is_backward(header)) {
     error("The offset are already reversed.");
@@ -108,9 +108,9 @@ void logger_dump_reverse_offset(struct logger_dump *dump) {
     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)) {}
+  for(size_t offset_debug = header->offset_first_record;
+      offset_debug < log->log.file_size;
+      offset_debug = tools_check_record_consistency(reader, offset_debug)) {}
 
   if (reader->verbose > 0) {
     message("Check done");
@@ -120,14 +120,14 @@ void logger_dump_reverse_offset(struct logger_dump *dump) {
   /* reverse header offset */
   header_change_offset_direction(header, logger_offset_corrupted);
   
-  /* reverse chunks */
+  /* reverse record */
   if (reader->verbose > 0) {
     message("Reversing offsets...");
   }
 
-  for(size_t offset = header->offset_first;
-      offset < dump->dump.file_size;
-      offset = tools_reverse_offset(header, dump->dump.map, offset)) {}
+  for(size_t offset = header->offset_first_record;
+      offset < log->log.file_size;
+      offset = tools_reverse_offset(header, log->log.map, offset)) {}
 
   if (reader->verbose > 0) {
     message("Reversing done");
@@ -142,9 +142,9 @@ void logger_dump_reverse_offset(struct logger_dump *dump) {
     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)) {}
+  for(size_t offset_debug = header->offset_first_record;
+      offset_debug < log->log.file_size;
+      offset_debug = tools_check_record_consistency(reader, offset_debug)) {}
 
   if (reader->verbose > 0) {
     message("Check done");

logger/logger_dump.h → logger/logger_logfile.h

@@ -17,10 +17,10 @@
  *
  ******************************************************************************/
 /**
- * @brief This file contains the high level function for the dump.
+ * @brief This file contains the high level function for the log.
  */
-#ifndef __LOGGER_LOGGER_DUMP_H__
-#define __LOGGER_LOGGER_DUMP_H__
+#ifndef __LOGGER_LOGGER_LOGFILE_H__
+#define __LOGGER_LOGGER_LOGFILE_H__
 
 #include "logger_header.h"
 #include "logger_time.h"
@@ -28,22 +28,22 @@
 struct logger_reader;
 
 /**
- * @brief This structure deals with the dump file.
+ * @brief This structure deals with the log file.
  *
  * TODO
  */
-struct logger_dump {
+struct logger_logfile {
 
   /* Information contained in the file header. */
   struct header header;
 
-  /* The reader that is using this dump. */
+  /* The reader that is using this log file. */
   struct logger_reader *reader;
 
-  /* Information about the time chunks */
+  /* Information about the time records */
   struct time_array times;
 
-  /* The dump's variables. */
+  /* The log's variables. */
   struct {
     /* Mapped data */
     void *map;
@@ -51,13 +51,13 @@ struct logger_dump {
     /* File size */
     size_t file_size;
 
-  } dump;
+  } log;
 
 };
 
 
-void logger_dump_init(struct logger_dump *dump, char *filename, struct logger_reader *reader);
-void logger_dump_reverse_offset(struct logger_dump *dump);
-void logger_dump_free(struct logger_dump *dump);
+void logger_logfile_init(struct logger_logfile *log, char *filename, struct logger_reader *reader);
+void logger_logfile_reverse_offset(struct logger_logfile *log);
+void logger_logfile_free(struct logger_logfile *log);
 
-#endif // __LOGGER_LOGGER_DUMP_H__
+#endif // __LOGGER_LOGGER_LOGFILE_H__

logger/logger_particle.c

@@ -64,7 +64,7 @@ void logger_particle_init(struct logger_particle *part) {
 }
 
 /**
- * @brief Read a single field for a particle.
+ * @brief Read a single named entry for a particle.
  *
  * @param part The #logger_particle to update.
  * @param map The mapped data.
@@ -79,6 +79,7 @@ size_t logger_particle_read_field(struct logger_particle *part, void *map,
 				  const size_t size) {
   void *p = NULL;
 
+  /* Get the correct pointer */
   if (strcmp("positions", field) == 0) {
     p = &part->pos;
   } else if (strcmp("velocities", field) == 0) {
@@ -97,8 +98,10 @@ size_t logger_particle_read_field(struct logger_particle *part, void *map,
     error("Type %s not defined", field);
   }
 
+  /* read the data */
   offset = io_read_data(map, size, p, offset);
 
+  /* Split the required fields */
   if (strcmp("consts", field) == 0) {
     part->mass = 0;
     part->id = 0;
@@ -113,13 +116,12 @@ size_t logger_particle_read_field(struct logger_particle *part, void *map,
 }
 
 /**
- * @brief Read a particle in the dump file.
+ * @brief Read a particle entry in the log file.
  *
  * @param reader The #logger_reader.
  * @param part The #logger_particle to update.
- * @param offset offset of the chunk to read.
- * @param time time to interpolate (if #logger_reader_type is an interpolating
- * one).
+ * @param offset offset of the record to read.
+ * @param time time to interpolate.
  * @param reader_type #logger_reader_type.
  *
  * @return position after the record.
@@ -128,10 +130,10 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
 			    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 header *h = &reader->log.header;
+  void *map = reader->log.log.map;
 
-  const struct time_array *times = &reader->dump.times;
+  const struct time_array *times = &reader->log.times;
 
   size_t mask = 0;
   size_t h_offset = 0;
@@ -150,7 +152,7 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
   }
 
   if (times) {
-    /* move offset by 1 in order to be in the required chunk */
+    /* move offset by 1 in order to be in the required record */
     part->time = time_array_get_time(times, offset - 1);
   }
   else
@@ -194,9 +196,9 @@ size_t logger_particle_read(struct logger_particle *part, const struct logger_re
  * @param time interpolation time
  *
  */
-void logger_particle_interpolate(struct logger_particle *part_curr,
-                                 const struct logger_particle *part_next,
-                                 const double time) {
+void logger_particle_interpolate(
+    struct logger_particle *part_curr, const struct logger_particle *part_next,
+    const double time) {
 
   if (!part_curr) error("part_curr is NULL");
   if (!part_next) error("part_next is NULL");
@@ -206,7 +208,7 @@ void logger_particle_interpolate(struct logger_particle *part_curr,
     error("Wrong particle order (next before current)");
   if ((time < part_curr->time) || (part_next->time < time))
     error(
-        "Interpolating, not extrapolating (particle time: %f, "
+        "Cannot extrapolate (particle time: %f, "
         "interpolating time: %f, next particle time: %f)",
         part_curr->time, time, part_next->time);
 #endif

logger/logger_particle.h

@@ -26,21 +26,26 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#if defined(HYDRO_DIMENSION_1D)
+#define DIM 1
+#elif defined(HYDRO_DIMENSION_2D)
+#define DIM 2
+#elif defined(HYDRO_DIMENSION_3D)
 #define DIM 3
+#endif
 
 struct logger_reader;
 
 /**
- * @brief Store the data from a chunk.
+ * @brief Store the data from a record.
  *
  * This structure contains all the required fields
  * present in a file.
  *
- * As we need only a single particle, no need to keep
- * it small.
+ * As we need only a few particles, no need to keep it small.
  *
  * The particle is initialized with #logger_particle_init
- * and can be updated with a chunk through #logger_particle_read.
+ * and can be updated with a record through #logger_particle_read.
  *
  * In #logger_particle_read, we use #logger_particle_read_field on
  * each field and #logger_particle_interpolate if a linear

logger/logger_python_wrapper.c

@@ -33,11 +33,13 @@
 /**