Changeset 1729

Timestamp:

02/11/11 14:49:48 (7 months ago)

Author:

Tobias Richter

Message:

implement more hdf1.8 features to make external links visible

refs #290 #287

still some issues with actually having external links,
but everything else still works, so this is a good state
to commit anyway

Location:

trunk

Files:

• configure.ac (modified) (1 diff)
• include/napi5.h (modified) (1 diff)
• src/napi.c (modified) (4 diffs)
• src/napi5.c (modified) (36 diffs)

trunk/configure.ac

@@ -574 +574 @@
                 EXTRA_LDPATH="$EXTRA_LDPATH $HDF5_LDFLAGS"
                 HDF5_LDFLAGS="$HDF5_LDFLAGS -lhdf5 -lz"
-                HDF5_CPPFLAGS="-I$H5ROOT/include -DHDF5 -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Pinsert_vers=2 -DH5Pregister_vers=2 -DH5Rget_obj_type_vers=2 -DH5Tarray_create_vers=2 -DH5Tcommit_vers=2 -DH5Tget_array_dims_vers=2 -DH5Topen_vers=2"
+                HDF5_CPPFLAGS="-I$H5ROOT/include -DHDF5 -DH5_NO_DEPRECATED_SYMBOLS -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Pinsert_vers=2 -DH5Pregister_vers=2 -DH5Rget_obj_type_vers=2 -DH5Tarray_create_vers=2 -DH5Tcommit_vers=2 -DH5Tget_array_dims_vers=2 -DH5Topen_vers=2"
                 # HDF5_CPPFLAGS="-I$H5ROOT/include -DHDF5 -DH5_NO_DEPRECATED_SYMBOLS -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Pinsert_vers=2 -DH5Pregister_vers=2 -DH5Rget_obj_type_vers=2 -DH5Tarray_create_vers=2 -DH5Tcommit_vers=2 -DH5Tget_array_dims_vers=2 -DH5Topen_vers=2"
                 ;;

trunk/include/napi5.h

@@ -46 +46 @@
 void NX5assignFunctions(pNexusFunction fHandle);
 
-herr_t nxgroup_info(hid_t loc_id, const char *name, void *op_data);
 herr_t attr_info(hid_t loc_id, const char *name, const H5A_info_t *unused, void *opdata);
-herr_t group_info(hid_t loc_id, const char *name, void *opdata);
+herr_t group_info(hid_t loc_id, const char *name, const H5L_info_t *unused, void *opdata);
+herr_t nxgroup_info(hid_t loc_id, const char *name, const H5L_info_t *unused, void *op_data);
 
 #endif /* NAPI5_H */

trunk/src/napi.c

@@ -685 +685 @@
         return status;
       }
-      status = NXopenpath(fid,expath);
+      status = NXopenpath(fid, expath);
       NXgetgroupID(fid,&breakID);
       setCloseID(fileStack,breakID);
@@ -1570 +1570 @@
     necessary. This can happen with paths like ../
   */
-  if(strlen(name) < 1)
-  {
+  if (strlen(name) < 1) {
       return NX_OK;
   }
   
   NXinitgroupdir(hfil);
-  while(NXgetnextentry(hfil,name2,xclass,&datatype) != NX_EOD)
-  {
-    
+
+  while(NXgetnextentry(hfil, name2, xclass, &datatype) != NX_EOD)
+  {
     if(strcmp(name2,name) == 0)
     {
@@ -1584 +1583 @@
       {
         return NXopendata(hfil,name);
-      } 
-      else
-      {
+      } else {
         return NXopengroup(hfil,name,xclass);
       }
@@ -1617 +1614 @@
     if(strcmp(name2,name) == 0)
     {
-      if(strcmp(xclass,"SDS") == 0)
-      {
+      if(strcmp(xclass,"SDS") == 0) {
         return NX_EOD;
       } 

trunk/src/napi5.c

@@ -403 +403 @@
   }
   /*------------------------------------------------------------------------*/
-  NXstatus  NX5opengroup (NXhandle fid, CONSTCHAR *name, CONSTCHAR *nxclass)
+  NXstatus  NX5opengroup(NXhandle fid, CONSTCHAR *name, CONSTCHAR *nxclass)
   {
 
@@ -413 +413 @@
           
     pFile = NXI5assert (fid);
-    if (pFile->iCurrentG == 0)
-    {
+    if (pFile->iCurrentG == 0) {
       strcpy(pBuffer,name);
-    } 
-    else 
-    {
+    } else {
        sprintf(pBuffer,"%s/%s",pFile->name_tmp,name);
     }
-    iRet = H5Gopen(pFile->iFID,(const char *)pBuffer, H5P_DEFAULT);
+    iRet = H5Gopen(pFile->iFID, (const char *)pBuffer, H5P_DEFAULT);
     if (iRet < 0) {
       sprintf (pBuffer, "ERROR: group %s does not exist", pFile->name_tmp);
@@ -446 +443 @@
         }
         /* check contents of group attribute */
-        attr1 = H5Aopen_name(pFile->iCurrentG, "NX_class");
+        attr1 = H5Aopen_by_name(pFile->iCurrentG, ".", "NX_class", H5P_DEFAULT, H5P_DEFAULT);
         if (attr1 < 0)
         {
@@ -952 +949 @@
       H5Tset_size(aid1,datalen); 
     }         
-    iRet = H5Aopen_name(vid, name);
+    iRet = H5Aopen_by_name(vid, ".", name, H5P_DEFAULT, H5P_DEFAULT);
     if (iRet>0) {
       H5Aclose(iRet);
@@ -1144 +1141 @@
       return NX_ERROR;
     }
-    status = H5Aopen_name(dataID,name);
+    status = H5Aopen_by_name(dataID,".", name, H5P_DEFAULT, H5P_DEFAULT);
     if(status > 0)
     {
@@ -1179 +1176 @@
     char        linkTarget[1024];
     int         type = NX_CHAR;
+    hid_t       targetid;
 
     pFile = NXI5assert (fid);
@@ -1202 +1200 @@
     } 
 
-    H5Glink(pFile->iFID, H5G_LINK_HARD, sLink->targetPath, linkTarget);
+    //targetid = H5Oopen(pFile->iFID, sLink->targetPath, H5P_DEFAULT);
+    H5Lcreate_hard(pFile->iFID, sLink->targetPath, H5L_SAME_LOC, linkTarget, H5P_DEFAULT, H5P_DEFAULT);
+    //H5Oclose(targetid);
 
     return NX5settargetattribute(pFile,sLink);
@@ -1214 +1214 @@
     int         type = NX_CHAR;
     char        *itemName = NULL;
+    hid_t       targetid;
 
     pFile = NXI5assert (fid);
@@ -1247 +1248 @@
     } 
 
-    H5Glink(pFile->iFID, H5G_LINK_HARD, sLink->targetPath, linkTarget);
+    //targetid = H5Oopen(pFile->iFID, sLink->targetPath, H5P_DEFAULT);
+    H5Lcreate_hard(pFile->iFID, sLink->targetPath, H5L_SAME_LOC, linkTarget, H5P_DEFAULT, H5P_DEFAULT);
+    //H5Oclose(targetid);
 
     return NX5settargetattribute(pFile,sLink);
@@ -1283 +1286 @@
   /* Operator function. */
            
-  herr_t nxgroup_info(hid_t loc_id, const char *name, void *op_data)
-  {
-    H5G_stat_t statbuf;
-    pinfo self;
-    
-    self = (pinfo)op_data;
-    H5Gget_objinfo(loc_id, name, 0, &statbuf);
-    switch (statbuf.type) 
-    {
-      case H5G_GROUP: 
+  herr_t nxgroup_info(hid_t loc_id, const char *name, const H5L_info_t *statbuf, void *op_data)
+  {
+    pinfo self = (pinfo) op_data;
+    H5O_info_t object_info;
+    H5Oget_info_by_name(loc_id, name, &object_info, H5P_DEFAULT);
+    switch ((object_info).type) {
+      case H5O_TYPE_GROUP: 
          self->iname = strdup(name);
-         self->type = H5G_GROUP;
+         self->type = H5O_TYPE_GROUP;
          break;
-      case H5G_DATASET: 
+      case H5O_TYPE_DATASET: 
          self->iname = strdup(name);
-         self->type = H5G_DATASET;
+         self->type = H5O_TYPE_DATASET;
          break;
       default:
+         // TODO defaults to group. not what we would want?
          self->type=0;
          break;     
@@ -1310 +1311 @@
   /* Operator function. */
 
-  herr_t group_info1(hid_t loc_id, const char *name, void *opdata)
-  {
-    H5G_stat_t statbuf;
+  herr_t group_info1(hid_t loc_id, const char *name, const H5L_info_t *statbuf, void *opdata)
+  {
     int iNX = *((int*)opdata);
-    H5Gget_objinfo(loc_id, name, 0, &statbuf);
-    
-    switch (statbuf.type) 
-    {
-      case H5G_GROUP: 
+    H5O_info_t object_info;
+    H5Oget_info_by_name(loc_id, name, &object_info, H5P_DEFAULT);
+    switch ((object_info).type) {
+      case H5O_TYPE_GROUP: 
         iNX++;
         *((int*)opdata)=iNX;
         break;
-      case H5G_DATASET:
+      case H5O_TYPE_DATASET:
         iNX++;
         *((int*)opdata)=iNX;
@@ -1334 +1333 @@
   /*-------------------------------------------------------------------------*/
 
-  NXstatus  NX5getgroupinfo_recurse (NXhandle fid, int *iN, NXname pName, NXname pClass)
+  NXstatus  NX5getgroupinfo_recurse(NXhandle fid, int *iN, NXname pName, NXname pClass)
   {
     pNexusFile5 pFile;
-    hid_t       atype, attr_id;
+    hid_t       atype, attr_id, grp;
     char        data[64];
         
@@ -1346 +1345 @@
        strcpy (pClass, "NXroot");
        pFile->iNX=0;
-       H5Giterate(pFile->iFID,"/",0,group_info1,&pFile->iNX);
+       grp = H5Gopen(pFile->iFID,"/",H5P_DEFAULT);
+       H5Literate(grp, H5_INDEX_NAME, H5_ITER_INC, 0, group_info1, &pFile->iNX);
+       H5Gclose(grp);
        *iN=pFile->iNX;
     }
     else {
       strcpy (pName,pFile->name_ref);
-      attr_id = H5Aopen_name(pFile->iCurrentG,"NX_class");
+      attr_id = H5Aopen_by_name(pFile->iCurrentG,".", "NX_class", H5P_DEFAULT, H5P_DEFAULT);
       if (attr_id<0) {
          strcpy(pClass, NX_UNKNOWN_GROUP);
@@ -1360 +1361 @@
         strcpy(pClass,data);
         pFile->iNX=0;
-        H5Giterate(pFile->iFID,pFile->name_ref,0,group_info1, &pFile->iNX);
+        grp = H5Gopen(pFile->iFID,pFile->name_ref,H5P_DEFAULT);
+        H5Literate(grp, H5_INDEX_NAME, H5_ITER_INC, 0, group_info1, &pFile->iNX);
+        H5Gclose(grp);
         *iN=pFile->iNX;
         H5Aclose(attr_id);
@@ -1371 +1374 @@
 {
   int count = 0, type;
-  hsize_t numobj, i;
+  H5G_info_t numobj;
   
   herr_t status;
 
-  status = H5Gget_num_objs(loc_id, &numobj);
+  status = H5Gget_info(loc_id, &numobj);
   if(status < 0) {
     NXReportError("Internal error, failed to retrive no of objects");
@@ -1381 +1384 @@
   }
 
-  for(i = 0; i < numobj; i++){
-    type = H5Gget_objtype_by_idx(loc_id,i);
-    if(type == H5G_GROUP || type == H5G_DATASET){
-      count++;
-    }
-  }
+  count = numobj.nlinks;
   return count;
 }
@@ -1395 +1393 @@
     hid_t atype, attr_id, gid;
     char data[64];
-        
+
     pFile = NXI5assert (fid);
     /* check if there is a group open */
@@ -1407 +1405 @@
     else {
       strcpy (pName,pFile->name_ref);
-      attr_id = H5Aopen_name(pFile->iCurrentG,"NX_class");
+      attr_id = H5Aopen_by_name(pFile->iCurrentG,".", "NX_class", H5P_DEFAULT, H5P_DEFAULT);
       if (attr_id<0) {
          strcpy(pClass, NX_UNKNOWN_GROUP);
@@ -1574 +1572 @@
   /*-------------------------------------------------------------------------*/
 
-  NXstatus  NX5getnextentry (NXhandle fid,NXname name, NXname nxclass, int *datatype)
+  NXstatus  NX5getnextentry(NXhandle fid, NXname name, NXname nxclass, int *datatype)
   {
     pNexusFile5 pFile;
@@ -1580 +1578 @@
     herr_t      iRet;
     int         iPtype, i;
-    int         idx;
+    hsize_t     idx;
     H5T_class_t tclass;
     char        data[128];
@@ -1599 +1597 @@
        strcpy(pFile->name_ref,"/");
     }  
-    iRet=H5Giterate(pFile->iFID,pFile->name_ref,&idx,nxgroup_info,&op_data);
+    grp = H5Gopen(pFile->iFID, pFile->name_ref, H5P_DEFAULT);
+    // index can be wrong here
+    iRet=H5Literate(grp, H5_INDEX_NAME, H5_ITER_INC, &idx, nxgroup_info, &op_data);
+    H5Gclose(grp);
     strcpy(nxclass, NX_UNKNOWN_GROUP);
    
@@ -1607 +1608 @@
     */
     if (pFile->iCurrentG == 0) {
+        // if pFile->iCurrentG == 0 would not pFile->name_ref be "/" already, so we could skip that if statement ?
        pFile->iNX=0;
-       iRet_iNX = H5Giterate(pFile->iFID,"/",0,group_info1,&pFile->iNX);
+       grp = H5Gopen(pFile->iFID, "/", H5P_DEFAULT);
+       iRet_iNX=H5Literate(grp, H5_INDEX_NAME, H5_ITER_INC, 0, group_info1, &pFile->iNX);
+       H5Gclose(grp);
     } else {
       pFile->iNX=0;
-      iRet_iNX = H5Giterate(pFile->iFID,pFile->name_ref,0,group_info1, &pFile->iNX);
+      grp = H5Gopen(pFile->iFID, pFile->name_ref, H5P_DEFAULT);
+        // index can be wrong here
+      iRet_iNX=H5Literate(grp, H5_INDEX_NAME, H5_ITER_INC, 0, group_info1, &pFile->iNX);
+      H5Gclose(grp);
     }
     if (idx == pFile->iNX) {
+        // why 2?
        iRet_iNX = 2;   
     } 
@@ -1627 +1635 @@
           return NX_EOD;
         }         
-        if (op_data.type == H5G_GROUP)
-        {
+        if (op_data.type == H5O_TYPE_GROUP) {
           /*
             open group and find class name attribute 
@@ -1641 +1648 @@
            grp = H5Gopen(pFile->iFID,ph_name, H5P_DEFAULT);
            if (grp < 0) {
-              sprintf (pBuffer, "ERROR: group %s does not exist", ph_name);
-              NXReportError( pBuffer);
+              sprintf(pBuffer, "ERROR: group %s does not exist", ph_name);
+              NXReportError(pBuffer);
               return NX_ERROR;  
            }
-           attr1 = H5Aopen_name(grp, "NX_class");
+           attr1 = H5Aopen_by_name(grp,".",  "NX_class", H5P_DEFAULT, H5P_DEFAULT);
            if (attr1 < 0) {
               strcpy(nxclass, NX_UNKNOWN_GROUP);
@@ -1658 +1665 @@
            }
            H5Gclose(grp);
-        } else if (op_data.type==H5G_DATASET)
-        {
+        } else if (op_data.type==H5O_TYPE_DATASET) {
           /*
             open dataset and find type
@@ -1675 +1681 @@
          }
           return NX_OK;
-       } 
-       else
-       { 
+       } else { 
          /*
            we are at the end of the search: clear the data structure and reset 
@@ -1692 +1696 @@
             free(op_data.iname);
          } 
-         NXReportError( 
-                            "ERROR: Iteration (directory) was not successful");
+         NXReportError("ERROR: iterating through group not successful");
          return NX_ERROR;              
        }
@@ -1901 +1904 @@
      hsize_t idx, intern_idx=-1;
      int vid;
+     H5O_info_t oinfo;
 
      pFile = NXI5assert (fileid);
@@ -1909 +1913 @@
      idx=pFile->iAtt5.iCurrentIDX;
      iRet=0;
-     // TODO replace
-     intern_idx=H5Aget_num_attrs(vid);
+ 
+     H5Oget_info(vid, &oinfo);
+     intern_idx=oinfo.num_attrs;
      if(intern_idx == idx) {
        killAttVID(pFile,vid);
@@ -1917 +1922 @@
 
      if (intern_idx > idx) {
-       /* iRet=H5Aiterate(vid,&idx,attr_info,&iname); */
        iRet=H5Aiterate(vid,H5_INDEX_CRT_ORDER,H5_ITER_INC,&idx,attr_info,&iname);
      } else {
@@ -1943 +1947 @@
        strcpy(pName,"What is this?");
      }
-     pFile->iCurrentA = H5Aopen_name(vid, pName);
+     pFile->iCurrentA = H5Aopen_by_name(vid, ".", pName, H5P_DEFAULT, H5P_DEFAULT);
      atype  = H5Aget_type(pFile->iCurrentA);
      aspace = H5Aget_space(pFile->iCurrentA);
@@ -1962 +1966 @@
      H5Aclose(pFile->iCurrentA);
   
-     intern_idx=H5Aget_num_attrs(vid);
+     H5Oget_info(vid, &oinfo);
+     intern_idx=oinfo.num_attrs;
 
      killAttVID(pFile,vid);
@@ -1983 +1988 @@
 
      vid = getAttVID(pFile);
-     iNew = H5Aopen_name(vid, name);
+     iNew = H5Aopen_by_name(vid, ".", name, H5P_DEFAULT, H5P_DEFAULT);
      if (iNew < 0) {
        sprintf (pBuffer, "ERROR: attribute \"%s\" not found", name);
@@ -2028 +2033 @@
      pNexusFile5 pFile;
      char *iname = NULL; 
-     unsigned int idx;
+     hid_t idx;
      int vid;
+     H5O_info_t oinfo;
     
      pFile = NXI5assert (fid);
@@ -2037 +2043 @@
      vid = getAttVID(pFile);
 
-     idx=H5Aget_num_attrs(vid);
+     H5Oget_info(vid, &oinfo);
+     idx=oinfo.num_attrs;
      if (idx > 0) {
        if(pFile->iCurrentG > 0 && pFile->iCurrentD == 0){
@@ -2162 +2169 @@
       fHandle->nxinitattrdir=NX5initattrdir;
       fHandle->nxprintlink=NX5printlink;
-      fHandle->nxnativeexternallink=NX5nativeexternallink;
+//      fHandle->nxnativeexternallink=NX5nativeexternallink;
+      fHandle->nxnativeexternallink=NULL;
 }