Added conversion from unpacked integers to float/double.

Added tests for recompression (uncompress to int, compress int)
Added tests for conversion from unpacked integers to float/double.

8 files changed, 258 insertions, 53 deletions

diff --git a/include/compression/tng_compress.h b/include/compression/tng_compress.h
index 14786d1..5d43ffc 100644
--- a/include/compression/tng_compress.h
+++ b/include/compression/tng_compress.h
@@ -166,11 +166,21 @@ int DECLSPECDLLEXPORT tng_compress_uncompress_float(char *data,float *posvel);
 
 int DECLSPECDLLEXPORT tng_compress_uncompress_int(char *data,int *posvel, unsigned long *prec_hi, unsigned long *prec_lo);
 
+/* This converts a block of integers, as obtained from tng_compress_uncompress_int, to floating point values
+   either double precision or single precision. */
+void DECLSPECDLLEXPORT tng_compress_int_to_double(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo,
+						  int natoms,int nframes,
+						  double *posvel_double);
 
-   /* Compression algorithms (matching the original trajng
-      assignments) The compression backends require that some of the
-      algorithms must have the same value. */
+void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo,
+						 int natoms,int nframes,
+						 float *posvel_float);
 
+
+/* Compression algorithms (matching the original trajng
+   assignments) The compression backends require that some of the
+   algorithms must have the same value. */
+   
 #define TNG_COMPRESS_ALGO_STOPBIT 1
 #define TNG_COMPRESS_ALGO_TRIPLET 2
 #define TNG_COMPRESS_ALGO_BWLZH1  8
diff --git a/src/compression/tng_compress.c b/src/compression/tng_compress.c
index ed3fca9..1219f6a 100644
--- a/src/compression/tng_compress.c
+++ b/src/compression/tng_compress.c
@@ -1764,6 +1764,20 @@ int DECLSPECDLLEXPORT tng_compress_uncompress_int(char *data,int *posvel, unsign
     return 1;
 }
 
+void DECLSPECDLLEXPORT tng_compress_int_to_double(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo,
+						  int natoms,int nframes,
+						  double *posvel_double)
+{
+  unquantize(posvel_double,natoms,nframes,PRECISION(prec_hi,prec_lo),posvel_int);
+}
+
+void DECLSPECDLLEXPORT tng_compress_int_to_float(int *posvel_int,unsigned long prec_hi, unsigned long prec_lo,
+						 int natoms,int nframes,
+						 float *posvel_float)
+{
+  unquantize_float(posvel_float,natoms,nframes,(float)PRECISION(prec_hi,prec_lo),posvel_int);
+}
+
 static char *compress_algo_pos[TNG_COMPRESS_ALGO_MAX]={
   "Positions invalid algorithm",
   "Positions stopbits interframe",
diff --git a/src/tests/compression/CMakeLists.txt b/src/tests/compression/CMakeLists.txt
index 39c2078..694d27b 100644
--- a/src/tests/compression/CMakeLists.txt
+++ b/src/tests/compression/CMakeLists.txt
@@ -9,7 +9,7 @@ include_directories(${CMAKE_SOURCE_DIR}/include/compression)
 include_directories(${CMAKE_BINARY_DIR}/generated/)
 
 set(number 0)
-set(numtests 62)
+set(numtests 64)
 
 while( number LESS ${numtests})
 
diff --git a/src/tests/compression/test61.h b/src/tests/compression/test61.h
index 2b71cc8..373456d 100644
--- a/src/tests/compression/test61.h
+++ b/src/tests/compression/test61.h
@@ -21,5 +21,5 @@
 #define INTMAX1 10000
 #define INTMAX2 10000
 #define INTMAX3 10000
-#define NFRAMES 1000
-#define EXPECTED_FILESIZE 6986313.
+#define NFRAMES 100
+#define EXPECTED_FILESIZE 698801.
diff --git a/src/tests/compression/test62.h b/src/tests/compression/test62.h
index 4b9e122..c8a2b48 100644
--- a/src/tests/compression/test62.h
+++ b/src/tests/compression/test62.h
@@ -4,23 +4,23 @@
 #define ALGOTEST
 #define NATOMS 1000
 #define CHUNKY 100
-#define SCALE 0.01 /* Changed on purpose. */
+#define SCALE 0.1
 #define PRECISION 0.01
 #define WRITEVEL 1
 #define VELPRECISION 0.1
-#define INITIALCODING -1
-#define INITIALCODINGPARAMETER -1
-#define CODING -1
-#define CODINGPARAMETER -1
-#define INITIALVELCODING -1
-#define INITIALVELCODINGPARAMETER -1
-#define VELCODING -1
-#define VELCODINGPARAMETER -1
+#define INITIALCODING 10
+#define INITIALCODINGPARAMETER 0
+#define CODING 10
+#define CODINGPARAMETER 0
+#define INITIALVELCODING 3
+#define INITIALVELCODINGPARAMETER 0
+#define VELCODING 8
+#define VELCODINGPARAMETER 0
 #define INTMIN1 0
 #define INTMIN2 0
 #define INTMIN3 0
 #define INTMAX1 10000
 #define INTMAX2 10000
 #define INTMAX3 10000
-#define NFRAMES 1000
-#define EXPECTED_FILESIZE 6986313.
+#define NFRAMES 100
+#define EXPECTED_FILESIZE 151226.
diff --git a/src/tests/compression/test63.h b/src/tests/compression/test63.h
new file mode 100644
index 0000000..65a4768
--- /dev/null
+++ b/src/tests/compression/test63.h
@@ -0,0 +1,26 @@
+#define TESTNAME "Coding. Read int and convert to double."
+#define FILENAME "test63.tng_compress"
+#define ALGOTEST
+#define NATOMS 1000
+#define CHUNKY 100
+#define SCALE 0.1
+#define PRECISION 0.01
+#define WRITEVEL 1
+#define VELPRECISION 0.1
+#define INITIALCODING 5
+#define INITIALCODINGPARAMETER 0
+#define CODING 5
+#define CODINGPARAMETER 0
+#define INITIALVELCODING 3
+#define INITIALVELCODINGPARAMETER -1
+#define VELCODING 3
+#define VELCODINGPARAMETER -1
+#define INTMIN1 0
+#define INTMIN2 0
+#define INTMIN3 0
+#define INTMAX1 10000
+#define INTMAX2 10000
+#define INTMAX3 10000
+#define NFRAMES 100
+#define INTTODOUBLE
+#define EXPECTED_FILESIZE 698801.
diff --git a/src/tests/compression/test64.h b/src/tests/compression/test64.h
new file mode 100644
index 0000000..02f99b5
--- /dev/null
+++ b/src/tests/compression/test64.h
@@ -0,0 +1,27 @@
+#define TESTNAME "Coding. Read int and convert to float."
+#define FILENAME "test64.tng_compress"
+#define ALGOTEST
+#define NATOMS 1000
+#define CHUNKY 100
+#define SCALE 0.1
+#define PRECISION 0.01
+#define WRITEVEL 1
+#define VELPRECISION 0.1
+#define INITIALCODING 5
+#define INITIALCODINGPARAMETER 0
+#define CODING 5
+#define CODINGPARAMETER 0
+#define INITIALVELCODING 3
+#define INITIALVELCODINGPARAMETER -1
+#define VELCODING 3
+#define VELCODINGPARAMETER -1
+#define INTMIN1 0
+#define INTMIN2 0
+#define INTMIN3 0
+#define INTMAX1 10000
+#define INTMAX2 10000
+#define INTMAX3 10000
+#define NFRAMES 100
+#define INTTOFLOAT
+#define TEST_FLOAT
+#define EXPECTED_FILESIZE 698801.
diff --git a/src/tests/compression/testsuite.c b/src/tests/compression/testsuite.c
index e1b9710..3ed9f32 100644
--- a/src/tests/compression/testsuite.c
+++ b/src/tests/compression/testsuite.c
@@ -286,6 +286,8 @@ struct tng_file
   REAL *vel;
   int *ipos;
   int *ivel;
+  unsigned int prec_hi, prec_lo;
+  unsigned int velprec_hi, velprec_lo;
 };
 
 static size_t fwrite_int_le(int *x,FILE *f)
@@ -357,9 +359,7 @@ static struct tng_file *open_tng_file_write(char *filename,
 
 static struct tng_file *open_tng_file_write_int(char *filename,
 						int natoms,int chunky,
-						unsigned long prec_hi, unsigned long prec_lo,
 						int writevel,
-						unsigned long velprec_hi, unsigned long velprec_lo,
 						int initial_coding,
 						int initial_coding_parameter,
 						int coding,
@@ -377,10 +377,8 @@ static struct tng_file *open_tng_file_write_int(char *filename,
   tng_file->ivel=NULL;
   tng_file->nframes=0;
   tng_file->chunky=chunky;
-  tng_file->precision=precision;
   tng_file->natoms=natoms;
   tng_file->writevel=writevel;
-  tng_file->velprecision=velprecision;
   tng_file->initial_coding=initial_coding;
   tng_file->initial_coding_parameter=initial_coding_parameter;
   tng_file->coding=coding;
@@ -390,15 +388,17 @@ static struct tng_file *open_tng_file_write_int(char *filename,
   tng_file->velcoding=velcoding;
   tng_file->velcoding_parameter=velcoding_parameter;
   tng_file->speed=speed;
-  tng_file->pos=malloc(natoms*chunky*3*sizeof *tng_file->pos);
+  tng_file->ipos=malloc(natoms*chunky*3*sizeof *tng_file->ipos);
   tng_file->f=fopen(filename,"wb");
   if (writevel)
-    tng_file->vel=malloc(natoms*chunky*3*sizeof *tng_file->vel);
+    tng_file->ivel=malloc(natoms*chunky*3*sizeof *tng_file->ivel);
   fwrite_int_le(&natoms,tng_file->f);
   return tng_file;
 }
 
-static void flush_tng_frames(struct tng_file *tng_file)
+static void flush_tng_frames(struct tng_file *tng_file,
+			     unsigned long prec_hi, unsigned long prec_lo,
+			     unsigned long velprec_hi, unsigned long velprec_lo)
 {
   int algo[4];
   char *buf;
@@ -408,19 +408,27 @@ static void flush_tng_frames(struct tng_file *tng_file)
   algo[1]=tng_file->initial_coding_parameter;
   algo[2]=tng_file->coding;
   algo[3]=tng_file->coding_parameter;
+#ifdef RECOMPRESS
+  buf=tng_compress_pos_int(tng_file->ipos,
+			     tng_file->natoms,
+			     tng_file->nframes,
+			     prec_hi,prec_lo,
+			     tng_file->speed,algo,&nitems);  
+#else /* RECOMPRESS */
 #ifdef TEST_FLOAT
   buf=tng_compress_pos_float(tng_file->pos,
 			     tng_file->natoms,
 			     tng_file->nframes,
 			     tng_file->precision,
 			     tng_file->speed,algo,&nitems);
-#else  
+#else  /* TEST_FLOAT */
   buf=tng_compress_pos(tng_file->pos,
 		       tng_file->natoms,
 		       tng_file->nframes,
 		       tng_file->precision,
 		       tng_file->speed,algo,&nitems);
-#endif
+#endif  /* TEST_FLOAT */
+#endif /* RECOMPRESS */
   tng_file->initial_coding=algo[0];
   tng_file->initial_coding_parameter=algo[1];
   tng_file->coding=algo[2];
@@ -434,19 +442,27 @@ static void flush_tng_frames(struct tng_file *tng_file)
       algo[1]=tng_file->initial_velcoding_parameter;
       algo[2]=tng_file->velcoding;
       algo[3]=tng_file->velcoding_parameter;
+#ifdef RECOMPRESS
+      buf=tng_compress_vel_int(tng_file->ivel,
+			       tng_file->natoms,
+			       tng_file->nframes,
+			       velprec_hi,velprec_lo,
+			       tng_file->speed,algo,&nitems);
+#else /* RECOMPRESS */
 #ifdef TEST_FLOAT
       buf=tng_compress_vel_float(tng_file->vel,
 			   tng_file->natoms,
 			   tng_file->nframes,
 			   tng_file->velprecision,
 			   tng_file->speed,algo,&nitems);
-#else
+#else /* TEST_FLOAT */
       buf=tng_compress_vel(tng_file->vel,
 			   tng_file->natoms,
 			   tng_file->nframes,
 			   tng_file->velprecision,
 			   tng_file->speed,algo,&nitems);
-#endif
+#endif /* TEST_FLOAT */
+#endif /* RECOMPRESS */
       tng_file->initial_velcoding=algo[0];
       tng_file->initial_velcoding_parameter=algo[1];
       tng_file->velcoding=algo[2];
@@ -466,16 +482,35 @@ static void write_tng_file(struct tng_file *tng_file,
     memcpy(tng_file->vel+tng_file->nframes*tng_file->natoms*3,vel,tng_file->natoms*3*sizeof *tng_file->vel);
   tng_file->nframes++;
   if (tng_file->nframes==tng_file->chunky)
-    flush_tng_frames(tng_file);
+    flush_tng_frames(tng_file,0,0,0,0);
+}
+
+static void write_tng_file_int(struct tng_file *tng_file,
+			       int *ipos,int *ivel,
+			       unsigned long prec_hi, unsigned long prec_lo,
+			       unsigned long velprec_hi, unsigned long velprec_lo)
+{
+  memcpy(tng_file->ipos+tng_file->nframes*tng_file->natoms*3,ipos,tng_file->natoms*3*sizeof *tng_file->ipos);
+  if (tng_file->writevel)
+    memcpy(tng_file->ivel+tng_file->nframes*tng_file->natoms*3,ivel,tng_file->natoms*3*sizeof *tng_file->ivel);
+  tng_file->nframes++;
+  if (tng_file->nframes==tng_file->chunky)
+    flush_tng_frames(tng_file,prec_hi,prec_lo,velprec_hi,velprec_lo);
+  tng_file->prec_hi=prec_hi;
+  tng_file->prec_lo=prec_lo;
+  tng_file->velprec_hi=velprec_hi;
+  tng_file->velprec_lo=velprec_lo;
 }
 
 static void close_tng_file_write(struct tng_file *tng_file)
 {
   if (tng_file->nframes)
-    flush_tng_frames(tng_file);
+    flush_tng_frames(tng_file,tng_file->prec_hi,tng_file->prec_lo,tng_file->velprec_hi,tng_file->velprec_lo);
   fclose(tng_file->f);
   free(tng_file->pos);
   free(tng_file->vel);
+  free(tng_file->ipos);
+  free(tng_file->ivel);
   free(tng_file);
 }
 
@@ -500,6 +535,27 @@ static struct tng_file *open_tng_file_read(char *filename, int writevel)
   return tng_file;
 }
 
+static struct tng_file *open_tng_file_read_int(char *filename, int writevel)
+{
+  struct tng_file *tng_file=malloc(sizeof *tng_file);
+  tng_file->pos=NULL;
+  tng_file->vel=NULL;
+  tng_file->ipos=NULL;
+  tng_file->ivel=NULL;
+  tng_file->f=fopen(filename,"rb");
+  tng_file->nframes=0;
+  tng_file->nframes_delivered=0;
+  tng_file->writevel=writevel;
+  if (tng_file->f)
+    fread_int_le(&tng_file->natoms,tng_file->f);
+  else
+    {
+      free(tng_file);
+      tng_file=NULL;
+    }
+  return tng_file;
+}
+
 static int read_tng_file(struct tng_file *tng_file,
 			 REAL *pos,
 			 REAL *vel)
@@ -573,10 +629,55 @@ static int read_tng_file(struct tng_file *tng_file,
   return 0;
 }
 
+static int read_tng_file_int(struct tng_file *tng_file,
+			     int *ipos,
+			     int *ivel,
+			     unsigned long *prec_hi, unsigned long *prec_lo,
+			     unsigned long *velprec_hi, unsigned long *velprec_lo)
+{
+  if (tng_file->nframes==tng_file->nframes_delivered)
+    {
+      int nitems;
+      char *buf;
+      free(tng_file->ipos);
+      free(tng_file->ivel);
+      if (!fread_int_le(&tng_file->nframes,tng_file->f))
+	return 1;
+      if (!fread_int_le(&nitems,tng_file->f))
+	return 1;
+      buf=malloc(nitems);
+      if (!fread(buf,1,nitems,tng_file->f))
+	return 1;
+      tng_file->ipos=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->ipos);
+      if (tng_file->writevel)
+	tng_file->ivel=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->ivel);
+      tng_compress_uncompress_int(buf,tng_file->ipos,prec_hi,prec_lo);
+      free(buf);
+      if (tng_file->writevel)
+	{
+	  if (!fread_int_le(&nitems,tng_file->f))
+	    return 1;
+	  buf=malloc(nitems);
+	  if (!fread(buf,1,nitems,tng_file->f))
+	    return 1;
+	  tng_compress_uncompress_int(buf,tng_file->ivel,velprec_hi,velprec_lo);
+	  free(buf);
+	}
+      tng_file->nframes_delivered=0;
+    }
+  memcpy(ipos,tng_file->ipos+tng_file->nframes_delivered*tng_file->natoms*3,tng_file->natoms*3*sizeof *ipos);
+  if (tng_file->writevel)
+    memcpy(ivel,tng_file->ivel+tng_file->nframes_delivered*tng_file->natoms*3,tng_file->natoms*3*sizeof *ivel);
+  tng_file->nframes_delivered++;
+  return 0;
+}
+
 static void close_tng_file_read(struct tng_file *tng_file)
 {
   free(tng_file->vel);
   free(tng_file->pos);
+  free(tng_file->ivel);
+  free(tng_file->ipos);
   fclose(tng_file->f);
   free(tng_file);
 }
@@ -631,6 +732,17 @@ static int algotest()
   REAL *box2=malloc(NATOMS*STRIDE2*sizeof *box2);
   REAL *velbox2=malloc(NATOMS*STRIDE2*sizeof *velbox2);
 #endif
+#ifdef RECOMPRESS
+  void *dumpfile=open_tng_file_write_int(TNG_COMPRESS_FILES_DIR FILENAME,NATOMS,CHUNKY,
+				     WRITEVEL,
+				     INITIALCODING,
+				     INITIALCODINGPARAMETER,CODING,CODINGPARAMETER,
+				     INITIALVELCODING,INITIALVELCODINGPARAMETER,
+				     VELCODING,VELCODINGPARAMETER,SPEED);
+  void *dumpfile_recompress=open_tng_file_read_int(TNG_COMPRESS_FILES_DIR RECOMPRESS,WRITEVEL);
+  if (!dumpfile_recompress)
+    return 1;
+#else /* RECOMPRESS */
 #ifdef GEN
   void *dumpfile=open_tng_file_write(TNG_COMPRESS_FILES_DIR FILENAME,NATOMS,CHUNKY,
 				     PRECISION,WRITEVEL,VELPRECISION,
@@ -641,11 +753,7 @@ static int algotest()
 #else
   void *dumpfile=open_tng_file_read(TNG_COMPRESS_FILES_DIR FILENAME,WRITEVEL);
 #endif
-#ifdef RECOMPRESS
-  void *dumpfile_recompress=open_tng_file_read_int(TNG_COMPRESS_FILES_DIR RECOMPRESS,WRITEVEL);
-  if (!dumpfile_recompress)
-    return 1;
-#endif
+#endif /* RECOMPRESS */
   if (!dumpfile)
     return 1;
   for (i=0; i<9; i++)
@@ -655,35 +763,54 @@ static int algotest()
   H1[8]=INTMAX3*PRECISION*SCALE;
   for (i=startframe; i<endframe; i++)
     {
-#ifndef RECOMPRES
+#ifdef RECOMPRESS
+      unsigned long prec_hi, prec_lo;
+      unsigned long velprec_hi, velprec_lo;
+      if (read_tng_file_int(dumpfile_recompress,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo))
+	return 1;
+      write_tng_file_int(dumpfile,intbox,intvelbox,prec_hi,prec_lo,velprec_hi,velprec_lo);
+#else /* RECOMPRESS */
       genibox(intbox,i);
       realbox(intbox,box1,STRIDE1);
 #if WRITEVEL
       genivelbox(intvelbox,i);
       realvelbox(intvelbox,velbox1,STRIDE1);
 #endif
-#else
-#ifdef GEN
-      if (read_tng_file_int(dumpfile_recompress,intbox,intvelbox))
-	return 1;
-#else
-      if (read_tng_file(dumpfile_recompress,box1,velbox1))
-	return 1;
-#endif
-#endif
       time1=(REAL)i;
       lambda1=(REAL)(i+100);
 #ifdef GEN
-#ifdef RECOMPRESS
-      write_tng_file_int(dumpfile,intbox,intvelbox);
-#else
       write_tng_file(dumpfile,box1,velbox1);
+#else /* GEN */
+#ifdef INTTOFLOAT
+      unsigned long prec_hi, prec_lo;
+      unsigned long velprec_hi, velprec_lo;
+      readreturn=read_tng_file_int(dumpfile,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo);
+      if (!readreturn)
+	{
+	  tng_compress_int_to_float(intbox,prec_hi,prec_lo,NATOMS,1,box2);
+#if WRITEVEL
+	  tng_compress_int_to_float(intvelbox,velprec_hi,velprec_lo,NATOMS,1,velbox2);
 #endif
-#else
+	}
+#else /* INTTOFLOAT */
+#ifdef INTTODOUBLE
+      unsigned long prec_hi, prec_lo;
+      unsigned long velprec_hi, velprec_lo;
+      readreturn=read_tng_file_int(dumpfile,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo);
+      if (!readreturn)
+	{
+	  tng_compress_int_to_double(intbox,prec_hi,prec_lo,NATOMS,1,box2);
+#if WRITEVEL
+	  tng_compress_int_to_double(intvelbox,velprec_hi,velprec_lo,NATOMS,1,velbox2);
+#endif
+	}
+#else /* INTTODOUBLE */
       readreturn=read_tng_file(dumpfile,box2,velbox2);
+#endif /* INTTODOUBLE */
+#endif /* INTTOFLOAT */
       if (readreturn==1) /* general read error  */
 	return 1;
-#endif
+#endif /* GEN */
 #ifndef GEN
       /* Check for equality of boxes. */
       if (!equalarr(box1,box2,(REAL)PRECISION,NATOMS,3,STRIDE1,STRIDE2))
@@ -692,7 +819,8 @@ static int algotest()
       if (!equalarr(velbox1,velbox2,(REAL)VELPRECISION,NATOMS,3,STRIDE1,STRIDE2))
 	return 5;
 #endif
-#endif
+#endif /* GEN */
+#endif /* RECOMPRESS */
     }
 #ifdef GEN
   close_tng_file_write(dumpfile);
@@ -736,9 +864,9 @@ int main()
       exit(EXIT_FAILURE);
     }
 #ifdef GEN
-  printf("Tng compress testsuite generating test: %s\n",TESTNAME);
+  printf("Tng compress testsuite generating (writing) test: %s\n",TESTNAME);
 #else
-  printf("Tng compress testsuite running test: %s\n",TESTNAME);
+  printf("Tng compress testsuite running (reading) test: %s\n",TESTNAME);
 #endif
   testval=algotest();
   if (testval==0)