[svn-r19835] Bug fix - In the code of N-bit filter, one line (the last line of H5Znbit.c in H5Z_nbit_compress -

"*buffer_size = j + 1;" was mistakenly taken out by someone.  It is necessary to update the new size.  I
put it back and made 2 test cases for integer and float to verify the correct dataset size.

I'm bringing the fix from 1.8 branch.  The changes to configure.in, tools/misc, tools/lib, config, c++/test, and Makefile.am are only property changes.  

Tested on jam.  But I tested 1.8 on jam, heiwa, and amani.

2 files changed, 394 insertions, 7 deletions

diff --git a/src/H5Znbit.c b/src/H5Znbit.c
index bcdd549..263b2cd 100644
--- a/src/H5Znbit.c
+++ b/src/H5Znbit.c
@@ -1365,17 +1365,17 @@ static void H5Z_nbit_compress_one_compound(unsigned char *data, size_t data_offs
 static void H5Z_nbit_compress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
                               size_t *buffer_size, const unsigned parms[])
 {
-   /* i: index of data, j: index of buffer,
+   /* i: index of data, new_size: index of buffer,
       buf_len: number of bits to be filled in current byte */
-   size_t i, j, size;
+   size_t i, size;
+   size_t new_size = 0;
    int buf_len;
    parms_atomic p;
 
    /* must initialize buffer to be zeros */
-   for(j = 0; j < *buffer_size; j++) buffer[j] = 0;
+   HDmemset(buffer, 0, *buffer_size);
 
    /* initialization before the loop */
-   j = 0;
    buf_len = sizeof(unsigned char) * 8;
 
    switch(parms[3]) {
@@ -1387,14 +1387,14 @@ static void H5Z_nbit_compress(unsigned char *data, unsigned d_nelmts, unsigned c
            p.offset = parms[7];
 
            for(i = 0; i < d_nelmts; i++) {
-              H5Z_nbit_compress_one_atomic(data, i*p.size, buffer, &j, &buf_len, p);
+              H5Z_nbit_compress_one_atomic(data, i*p.size, buffer, &new_size, &buf_len, p);
            }
            break;
       case H5Z_NBIT_ARRAY:
            size = parms[4];
            parms_index = 4;
            for(i = 0; i < d_nelmts; i++) {
-              H5Z_nbit_compress_one_array(data, i*size, buffer, &j, &buf_len, parms);
+              H5Z_nbit_compress_one_array(data, i*size, buffer, &new_size, &buf_len, parms);
               parms_index = 4;
            }
            break;
@@ -1402,10 +1402,14 @@ static void H5Z_nbit_compress(unsigned char *data, unsigned d_nelmts, unsigned c
            size = parms[4];
            parms_index = 4;
            for(i = 0; i < d_nelmts; i++) {
-              H5Z_nbit_compress_one_compound(data, i*size, buffer, &j, &buf_len, parms);
+              H5Z_nbit_compress_one_compound(data, i*size, buffer, &new_size, &buf_len, parms);
               parms_index = 4;
            }
            break;
    } /* end switch */
+
+   /* Update the size to the new value after compression.  If there are any bits hanging over in
+    * the last byte, increment the value by 1. */
+   *buffer_size = new_size + 1;
 }
 #endif /* H5_HAVE_FILTER_NBIT */
diff --git a/test/dsets.c b/test/dsets.c
index 1d81e1d..682dfce 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -53,6 +53,7 @@ const char *FILENAME[] = {
     NULL
 };
 #define FILENAME_BUF_SIZE       1024
+#define KB                      1024
 
 #define FILE_DEFLATE_NAME       "deflate.h5"
 
@@ -99,6 +100,8 @@ const char *FILENAME[] = {
 #define DSET_NBIT_COMPOUND_NAME        "nbit_compound"
 #define DSET_NBIT_COMPOUND_NAME_2      "nbit_compound_2"
 #define DSET_NBIT_COMPOUND_NAME_3      "nbit_compound_3"
+#define DSET_NBIT_INT_SIZE_NAME        "nbit_int_size"
+#define DSET_NBIT_FLT_SIZE_NAME        "nbit_flt_size"
 #define DSET_SCALEOFFSET_INT_NAME      "scaleoffset_int"
 #define DSET_SCALEOFFSET_INT_NAME_2    "scaleoffset_int_2"
 #define DSET_SCALEOFFSET_FLOAT_NAME    "scaleoffset_float"
@@ -3946,6 +3949,384 @@ error:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    test_nbit_int_size
+ *
+ * Purpose:     Tests the correct size of the integer datatype for nbit filter
+ *
+ * Return:      Success:        0
+ *
+ *              Failure:        -1
+ *
+ * Programmer:  Raymond Lu
+ *              19 November 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+test_nbit_int_size(hid_t file)
+{
+#ifdef H5_HAVE_FILTER_NBIT
+    hid_t   dataspace, dataset, datatype, mem_datatype, dset_create_props;
+    hsize_t dims[2], chunk_size[2];
+    hsize_t dset_size = 0;
+    int     orig_data[DSET_DIM1][DSET_DIM2];
+    int     i, j;
+    size_t  precision, offset;
+#else /* H5_HAVE_FILTER_NBIT */
+    const char          *not_supported= "    Nbit is not enabled.";
+#endif /* H5_HAVE_FILTER_NBIT */
+
+    TESTING("    nbit integer dataset size");
+#ifdef H5_HAVE_FILTER_NBIT
+
+   /* Define dataset datatype (integer), and set precision, offset */
+   if((datatype = H5Tcopy(H5T_NATIVE_INT)) < 0) {
+       H5_FAILED();
+       printf("    line %d: H5Tcopy failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   precision = 16; /* precision includes sign bit */
+   if(H5Tset_precision(datatype,precision)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_precision failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   offset = 8;
+   if(H5Tset_offset(datatype,offset)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Tset_offset failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   /* Copy to memory datatype */
+   if((mem_datatype = H5Tcopy(datatype)) < 0) {
+       H5_FAILED();
+       printf("    line %d: H5Tcopy failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   /* Set order of dataset datatype */
+   if(H5Tset_order(datatype, H5T_ORDER_BE)<0) {
+        H5_FAILED();
+       printf("    line %d: H5Pset_order failed\n",__LINE__);
+       goto error;
+   } /* end if */
+  
+   if(H5Tset_size(datatype, 4)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_size failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /* Initiliaze data buffer with random data within correct range
+   * corresponding to the memory datatype's precision and offset.
+   */
+   for (i=0; i < DSET_DIM1; i++)
+       for (j=0; j < DSET_DIM2; j++)
+           orig_data[i][j] = rand() % (int)pow(2, precision-1) <<offset;
+
+
+   /* Describe the dataspace. */
+   dims[0] = DSET_DIM1;
+   dims[1] = DSET_DIM2;
+   if((dataspace = H5Screate_simple (2, dims, NULL))<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pcreate failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Set the dataset creation property list to specify the chunks
+   */
+   chunk_size[0] = DSET_DIM1/10;
+   chunk_size[1] = DSET_DIM2/10;
+   if((dset_create_props = H5Pcreate (H5P_DATASET_CREATE))<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pcreate failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   if(H5Pset_chunk (dset_create_props, 2, chunk_size)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_chunk failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Set for n-bit compression
+   */
+   if(H5Pset_nbit (dset_create_props)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_nbit failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Create a new dataset within the file.
+   */
+   if((dataset = H5Dcreate2 (file, DSET_NBIT_INT_SIZE_NAME, datatype,
+                            dataspace, H5P_DEFAULT, 
+                            dset_create_props, H5P_DEFAULT))<0) {
+       H5_FAILED();
+       printf("    line %d: H5dwrite failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Write the array to the file.
+   */
+   if(H5Dwrite (dataset, mem_datatype, H5S_ALL, H5S_ALL,
+                H5P_DEFAULT, orig_data)<0) {
+       H5_FAILED();
+       printf("    Line %d: H5Dwrite failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   /* 
+    * Get the precision of the data type
+    */
+   if((precision = H5Tget_precision(datatype)) == 0) {
+       H5_FAILED();
+       printf("    Line %d: wrong precision size: %d\n",__LINE__, precision);
+       goto error;
+   } /* end if */
+
+   /* 
+    * The size of the dataset after compression should around 2 * DSET_DIM1 * DSET_DIM2
+    */
+   if((dset_size = H5Dget_storage_size(dataset)) < DSET_DIM1*DSET_DIM2*(precision/8) || 
+       dset_size > DSET_DIM1*DSET_DIM2*(precision/8) + 1*KB) {
+       H5_FAILED();
+       printf("    Line %d: wrong dataset size: %d\n",__LINE__, dset_size);
+       goto error;
+   } /* end if */
+
+   H5Tclose (datatype);
+   H5Tclose (mem_datatype);
+   H5Dclose (dataset);
+   H5Sclose (dataspace);
+   H5Pclose (dset_create_props);
+
+    PASSED();
+#else
+    SKIPPED();
+    puts(not_supported);
+#endif
+
+   return 0;
+error:
+    return -1;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    test_nbit_flt_size
+ *
+ * Purpose:     Tests the correct size of the floating-number datatype for 
+ *              nbit filter
+ *
+ * Return:      Success:        0
+ *
+ *              Failure:        -1
+ *
+ * Programmer:  Raymond Lu
+ *              19 November 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+test_nbit_flt_size(hid_t file)
+{
+#ifdef H5_HAVE_FILTER_NBIT
+    hid_t   dataspace, dataset, datatype, dset_create_props;
+    hsize_t dims[2], chunk_size[2];
+    hsize_t dset_size = 0;
+    float   orig_data[DSET_DIM1][DSET_DIM2];
+    int     i, j;
+    size_t  precision, offset;
+    size_t  spos, epos, esize, mpos, msize;
+#else /* H5_HAVE_FILTER_NBIT */
+    const char          *not_supported= "    Nbit is not enabled.";
+#endif /* H5_HAVE_FILTER_NBIT */
+
+    TESTING("    nbit floating-number dataset size");
+#ifdef H5_HAVE_FILTER_NBIT
+
+  /* Define floating-point type for dataset
+   *-------------------------------------------------------------------
+   * size=4 byte, precision=16 bits, offset=8 bits,
+   * mantissa size=9 bits, mantissa position=8,
+   * exponent size=6 bits, exponent position=17,
+   * exponent bias=31.
+   * It can be illustrated in little-endian order as:
+   * (S - sign bit, E - exponent bit, M - mantissa bit,
+   *  ? - padding bit)
+   *
+   *           3        2        1        0
+   *       ???????? SEEEEEEM MMMMMMMM ????????
+   *
+   * To create a new floating-point type, the following
+   * properties must be set in the order of
+   *     set fields -> set offset -> set precision -> set size.
+   * All these properties must be set before the type can function.
+   * Other properties can be set anytime. Derived type size cannot
+   * be expanded bigger than original size but can be decreased.
+   * There should be no holes among the significant bits. Exponent
+   * bias usually is set 2^(n-1)-1, where n is the exponent size.
+   *-------------------------------------------------------------------*/
+   if((datatype = H5Tcopy(H5T_IEEE_F32LE)) < 0) {
+       H5_FAILED();
+       printf("    line %d: H5Tcopy failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   msize = 9;
+   spos = 23;
+   epos = 17;
+   esize = 6;
+   mpos = 8;
+   offset = 8;
+   precision = 16;
+
+   if(H5Tset_fields(datatype, spos, epos, esize, mpos, msize)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Tset_fields failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   if(H5Tset_offset(datatype,offset)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Tset_offset failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   if(H5Tset_precision(datatype,precision)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Tset_precision failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   if(H5Tset_size(datatype, 4)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_size failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   /* Set order of dataset datatype */
+   if(H5Tset_order(datatype, H5T_ORDER_BE)<0) {
+        H5_FAILED();
+       printf("    line %d: H5Pset_order failed\n",__LINE__);
+       goto error;
+   } /* end if */
+  
+   if(H5Tset_ebias(datatype, 31)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_size failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /* 
+   * Initiliaze data buffer with random data 
+   */
+   for (i=0; i < DSET_DIM1; i++)
+       for (j=0; j < DSET_DIM2; j++)
+           orig_data[i][j] = (rand() % 1234567) / 2;
+
+
+   /* Describe the dataspace. */
+   dims[0] = DSET_DIM1;
+   dims[1] = DSET_DIM2;
+   if((dataspace = H5Screate_simple (2, dims, NULL))<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pcreate failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Set the dataset creation property list to specify the chunks
+   */
+   chunk_size[0] = DSET_DIM1/10;
+   chunk_size[1] = DSET_DIM2/10;
+   if((dset_create_props = H5Pcreate (H5P_DATASET_CREATE))<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pcreate failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   if(H5Pset_chunk (dset_create_props, 2, chunk_size)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_chunk failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Set for n-bit compression
+   */
+   if(H5Pset_nbit (dset_create_props)<0) {
+       H5_FAILED();
+       printf("    line %d: H5Pset_nbit failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Create a new dataset within the file.
+   */
+   if((dataset = H5Dcreate2 (file, DSET_NBIT_FLT_SIZE_NAME, datatype,
+                            dataspace, H5P_DEFAULT, 
+                            dset_create_props, H5P_DEFAULT))<0) {
+       H5_FAILED();
+       printf("    line %d: H5dwrite failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+  /*
+   * Write the array to the file.
+   */
+   if(H5Dwrite (dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
+                H5P_DEFAULT, orig_data)<0) {
+       H5_FAILED();
+       printf("    Line %d: H5Dwrite failed\n",__LINE__);
+       goto error;
+   } /* end if */
+
+   /* 
+    * Get the precision of the data type
+    */
+   if((precision = H5Tget_precision(datatype)) == 0) {
+       H5_FAILED();
+       printf("    Line %d: wrong precision size: %d\n",__LINE__, precision);
+       goto error;
+   } /* end if */
+
+   /* 
+    * The size of the dataset after compression should around 2 * DSET_DIM1 * DSET_DIM2
+    */
+   if((dset_size = H5Dget_storage_size(dataset)) < DSET_DIM1*DSET_DIM2*(precision/8) || 
+       dset_size > DSET_DIM1*DSET_DIM2*(precision/8) + 1*KB) {
+       H5_FAILED();
+       printf("    Line %d: wrong dataset size: %d\n",__LINE__, dset_size);
+       goto error;
+   } /* end if */
+
+   H5Tclose (datatype);
+   H5Dclose (dataset);
+   H5Sclose (dataspace);
+   H5Pclose (dset_create_props);
+
+    PASSED();
+#else
+    SKIPPED();
+    puts(not_supported);
+#endif
+
+   return 0;
+error:
+    return -1;
+}
+
+/*-------------------------------------------------------------------------
  * Function:    test_scaleoffset_int
  *
  * Purpose:     Tests the integer datatype for scaleoffset filter
@@ -7853,6 +8234,8 @@ main(void)
         nerrors += (test_nbit_compound(file) < 0 		? 1 : 0);
         nerrors += (test_nbit_compound_2(file) < 0 		? 1 : 0);
         nerrors += (test_nbit_compound_3(file) < 0 		? 1 : 0);
+        nerrors += (test_nbit_int_size(file) < 0 		? 1 : 0);
+        nerrors += (test_nbit_flt_size(file) < 0 		? 1 : 0);
         nerrors += (test_scaleoffset_int(file) < 0 		? 1 : 0);
         nerrors += (test_scaleoffset_int_2(file) < 0 	? 1 : 0);
         nerrors += (test_scaleoffset_float(file) < 0 	? 1 : 0);