[svn-r17077] merge 17076 from trunk

bug fix: h5repack was not applying a requested contiguous layout for a dataset with filters
added a test to the C program test (not to the script), that verifies the layout and filters

tested: linux

3 files changed, 88 insertions, 67 deletions

diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index ee9621d..6b08a2f 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -42,10 +42,10 @@ int aux_find_obj(const char* name,          /* object name from traverse list */
          *obj =  options->op_tbl->objs[i];
          return i;
      }
-     
+
      pdest  = strstr(name,options->op_tbl->objs[i].path);
      result = (int)(pdest - name);
-     
+
      /* found at position 1, meaning without '/' */
      if( pdest != NULL && result==1 )
      {
@@ -73,19 +73,19 @@ int aux_assign_obj(const char* name,            /* object name from traverse lis
                    pack_opt_t *options,         /* repack options */
                    pack_info_t *obj /*OUT*/)    /* info about object to filter */
 {
-    
+
     int  idx, i;
     pack_info_t tmp;
-    
+
     init_packobject(&tmp);
-    
+
     idx = aux_find_obj(name,options,&tmp);
-    
+
     /* name was on input */
     if (idx>=0)
     {
-        
-        
+
+
         /* applying to all objects */
         if (options->all_layout)
         {
@@ -125,9 +125,9 @@ int aux_assign_obj(const char* name,            /* object name from traverse lis
             default:
                 break;
             }/*switch*/
-            
+
         }
-        
+
         /* applying to all objects */
         if (options->all_filter)
         {
@@ -143,16 +143,16 @@ int aux_assign_obj(const char* name,            /* object name from traverse lis
                 tmp.filter[i] = options->op_tbl->objs[idx].filter[i];
             }
         }
-        
-        
+
+
     } /* if idx */
-    
-    
+
+
     /* no input name */
-    
+
     else
     {
-        
+
         if (options->all_filter)
         {
             int k;
@@ -183,11 +183,11 @@ int aux_assign_obj(const char* name,            /* object name from traverse lis
             }/*switch*/
         }
     }
-    
+
     *obj = tmp;
     return 1;
-    
-}       
+
+}
 
 
 /*-------------------------------------------------------------------------
@@ -223,40 +223,40 @@ int apply_filters(const char* name,    /* object name from traverse list */
     pack_info_t  obj;
 
     *has_filter = 0;
-    
+
     if (rank==0) /* scalar dataset, do not apply */
         return 0;
-    
+
    /*-------------------------------------------------------------------------
     * initialize the assigment object
     *-------------------------------------------------------------------------
     */
     init_packobject(&obj);
-    
+
    /*-------------------------------------------------------------------------
     * find options
     *-------------------------------------------------------------------------
     */
     if (aux_assign_obj(name,options,&obj)==0)
         return 0;
-    
+
     /* get information about input filters */
     if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
         return -1;
-    
+
    /*-------------------------------------------------------------------------
     * check if we have filters in the pipeline
     * we want to replace them with the input filters
     * only remove if we are inserting new ones
     *-------------------------------------------------------------------------
     */
-    if (nfilters && obj.nfilters ) 
+    if (nfilters && obj.nfilters )
     {
         *has_filter = 1;
         if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
             return -1;
     }
-    
+
    /*-------------------------------------------------------------------------
     * check if there is an existent chunk
     * read it only if there is not a requested layout
@@ -266,7 +266,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
     {
         if ((layout = H5Pget_layout(dcpl_id))<0)
             return -1;
-        
+
         if (layout == H5D_CHUNKED)
         {
             if ((rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize/*out*/))<0)
@@ -277,7 +277,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
                 obj.chunk.chunk_lengths[i] = chsize[i];
         }
     }
-    
+
     /*-------------------------------------------------------------------------
     * the type of filter and additional parameter
     * type can be one of the filters
@@ -290,10 +290,10 @@ int apply_filters(const char* name,    /* object name from traverse list */
     * H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
     *-------------------------------------------------------------------------
     */
-    
+
     if (obj.nfilters)
     {
-        
+
    /*-------------------------------------------------------------------------
     * filters require CHUNK layout; if we do not have one define a default
     *-------------------------------------------------------------------------
@@ -332,14 +332,14 @@ int apply_filters(const char* name,    /* object name from traverse list */
             }
 
         }
-        
+
         for ( i=0; i<obj.nfilters; i++)
         {
             switch (obj.filter[i].filtn)
             {
             default:
                 break;
-                
+
            /*-------------------------------------------------------------------------
             * H5Z_FILTER_DEFLATE       1 , deflation like gzip
             *-------------------------------------------------------------------------
@@ -347,7 +347,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
             case H5Z_FILTER_DEFLATE:
                 {
                     unsigned     aggression;     /* the deflate level */
-                    
+
                     aggression = obj.filter[i].cd_values[0];
                     /* set up for deflated data */
                     if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
@@ -356,7 +356,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
                         return -1;
                 }
                 break;
-                
+
            /*-------------------------------------------------------------------------
             * H5Z_FILTER_SZIP       4 , szip compression
             *-------------------------------------------------------------------------
@@ -365,19 +365,19 @@ int apply_filters(const char* name,    /* object name from traverse list */
                 {
                     unsigned  options_mask;
                     unsigned  pixels_per_block;
-                    
+
                     options_mask     = obj.filter[i].cd_values[0];
                     pixels_per_block = obj.filter[i].cd_values[1];
-                    
+
                     /* set up for szip data */
                     if(H5Pset_chunk(dcpl_id,obj.chunk.rank,obj.chunk.chunk_lengths)<0)
                         return -1;
                     if (H5Pset_szip(dcpl_id,options_mask,pixels_per_block)<0)
                         return -1;
-                    
+
                 }
                 break;
-                
+
            /*-------------------------------------------------------------------------
             * H5Z_FILTER_SHUFFLE    2 , shuffle the data
             *-------------------------------------------------------------------------
@@ -388,7 +388,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
                 if (H5Pset_shuffle(dcpl_id)<0)
                     return -1;
                 break;
-                
+
            /*-------------------------------------------------------------------------
             * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
             *-------------------------------------------------------------------------
@@ -413,15 +413,15 @@ int apply_filters(const char* name,    /* object name from traverse list */
              * H5Z_FILTER_SCALEOFFSET , scale+offset compression
              *-------------------------------------------------------------------------
              */
-                
+
             case H5Z_FILTER_SCALEOFFSET:
                 {
                     H5Z_SO_scale_type_t scale_type;
                     int                 scale_factor;
-                    
+
                     scale_type   = obj.filter[i].cd_values[0];
                     scale_factor = obj.filter[i].cd_values[1];
-                    
+
                     if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
                         return -1;
                     if (H5Pset_scaleoffset(dcpl_id,scale_type,scale_factor)<0)
@@ -430,30 +430,38 @@ int apply_filters(const char* name,    /* object name from traverse list */
                 break;
             } /* switch */
         }/*i*/
-        
+
     }
     /*obj.nfilters*/
-    
+
     /*-------------------------------------------------------------------------
     * layout
     *-------------------------------------------------------------------------
     */
-    
+
     if (obj.layout>=0)
     {
         /* a layout was defined */
         if (H5Pset_layout(dcpl_id, obj.layout)<0)
             return -1;
-        
-        if (H5D_CHUNKED==obj.layout) { /* set up chunk */
+
+        if (H5D_CHUNKED == obj.layout) 
+        { 
             if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
                 return -1;
         }
-        else if (H5D_COMPACT==obj.layout) {
+        else if (H5D_COMPACT == obj.layout) 
+        {
             if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY)<0)
                 return -1;
         }
-        
+        /* remove filters for the H5D_CONTIGUOUS case */
+        else if (H5D_CONTIGUOUS == obj.layout) 
+        {
+            if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
+                return -1;
+        }
+
     }
 
  return 0;
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 92d758e..69df02c 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -18,8 +18,8 @@
 #include "h5tools_utils.h"
 
 extern char  *progname;
-static int has_layout(hid_t pid, pack_info_t *obj);
-static int has_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
+static int verify_layout(hid_t pid, pack_info_t *obj);
+static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
 
 
 /*-------------------------------------------------------------------------
@@ -82,7 +82,7 @@ int h5repack_verify(const char *fname,
         * filter check
         *-------------------------------------------------------------------------
         */
-        if(has_filters(pid, tid, obj->nfilters, obj->filter) <= 0)
+        if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0)
                 ok = 0;
 
 
@@ -90,7 +90,7 @@ int h5repack_verify(const char *fname,
         * layout check
         *-------------------------------------------------------------------------
         */
-        if((obj->layout != -1) && (has_layout(pid, obj) == 0))
+        if((obj->layout != -1) && (verify_layout(pid, obj) == 0))
             ok = 0;
 
        /*-------------------------------------------------------------------------
@@ -151,7 +151,7 @@ int h5repack_verify(const char *fname,
                 if(options->all_filter == 1)
                 {
 
-                    if(has_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0)
+                    if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0)
                         ok = 0;
                 }
 
@@ -165,7 +165,7 @@ int h5repack_verify(const char *fname,
                     init_packobject(&pack);
                     pack.layout = options->layout_g;
                     pack.chunk = options->chunk_g;
-                    if(has_layout(pid, &pack) == 0)
+                    if(verify_layout(pid, &pack) == 0)
                         ok = 0;
                 }
 
@@ -215,13 +215,13 @@ error:
 
 
 /*-------------------------------------------------------------------------
- * Function: has_layout
+ * Function: verify_layout
  *
  * Purpose: verify which layout is present in the property list DCPL_ID
  *
  *  H5D_COMPACT	  	= 0
  *  H5D_CONTIGUOUS	= 1
- *  H5D_CHUNKED		  = 2
+ *  H5D_CHUNKED		= 2
  *
  * Return: 1 has, 0 does not, -1 error
  *
@@ -232,8 +232,8 @@ error:
  *-------------------------------------------------------------------------
  */
 
-int has_layout(hid_t pid,
-               pack_info_t *obj)
+int verify_layout(hid_t pid,
+                  pack_info_t *obj)
 {
     hsize_t      chsize[64];     /* chunk size in elements */
     H5D_layout_t layout;         /* layout */
@@ -241,17 +241,13 @@ int has_layout(hid_t pid,
     int          rank;           /* rank */
     int          i;              /* index */
 
-    /* if no information about the input layout is requested return exit */
-    if (obj==NULL)
-        return 1;
-
     /* check if we have filters in the input object */
     if ((nfilters = H5Pget_nfilters(pid)) < 0)
         return -1;
 
-    /* a non chunked layout was requested on a filtered object; avoid the test */
+    /* a non chunked layout was requested on a filtered object */
     if (nfilters && obj->layout!=H5D_CHUNKED)
-        return 1;
+        return 0;
 
     /* get layout */
     if ((layout = H5Pget_layout(pid)) < 0)
@@ -458,7 +454,7 @@ error:
 
 
 /*-------------------------------------------------------------------------
- * Function: has_filters
+ * Function: verify_filters
  *
  * Purpose: verify if all requested filters in the array FILTER obtained
  *  from user input are present in the property list PID obtained from
@@ -477,7 +473,7 @@ error:
  */
 
 static 
-int has_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
+int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
 {
     int           nfilters_dcpl;  /* number of filters in DCPL*/
     unsigned      filt_flags;     /* filter flags */
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index af4d671..b36afde 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -659,6 +659,23 @@ int main (void)
     if (h5repack_end (&pack_options) < 0)
         GOERROR;
 
+    /*-------------------------------------------------------------------------
+    * do the same test for a file with filters (chunked)
+    *-------------------------------------------------------------------------
+    */
+    if (h5repack_init (&pack_options, 0) < 0)
+        GOERROR;
+    if (h5repack_addlayout("CONTI",&pack_options) < 0)
+        GOERROR;
+    if (h5repack(FNAME8,FNAME8OUT,&pack_options) < 0)
+        GOERROR;
+    if (h5diff(FNAME8,FNAME8OUT,NULL,NULL,&diff_options) >0)
+        GOERROR;
+    if (h5repack_verify(FNAME8OUT,&pack_options)<=0)
+        GOERROR;
+    if (h5repack_end (&pack_options) < 0)
+        GOERROR;
+
     PASSED();
 
     TESTING("    adding layout compact");